Molinism is a type of philosophical theology. It is a structure that wraps itself around Scripture in an attempt to make sense of the content. That is not a bad thing in and of itself. We employ our methods of reason for interpreting the world around us and the logical contructs of a systematic theology allow us to do that with the Bible. Every field of inquiry does this, not just theology. A systematic approach is how all science is done. Day-to-day commerce is similarly conducted within the framework of certain expectations and assumptions. Political entities also operate each within its own system. The Molinist system is just one of many used to interpret the world and God’s work.
The Molinist understanding of God’s knowledge is that He knows not only all that will take place but also everything that might have taken place. As William Lane Craig puts it, “God possesses knowledge of all true counterfactual propositions, including counterfactuals of creaturely freedom. That is to say, He knows what contingent states of affairs would obtain if certain antecedent states of affairs were to obtain; whereas by His natural knowledge God knew what any free creature could do in any set of circumstances, now in this second moment God knows what any free creature would do in any set of circumstances.” So God in His sovereignty initiates and manages the affairs of humanity in such a way so as to bring about His desired ends.
This is the result of a thing called “middle knowledge.” Middle knowledge comprises those choices which are available to human will, the difference between what a creature could do in any set of circumstances versus what the creature would do in any given set of circumstances. Dr. Craig explains further that
Middle knowledge is like natural knowledge in that such knowledge does not depend on any decision of the divine will; God does not determine which counterfactuals of creaturely freedom are true or false. Thus, if it is true that
If some agent S were placed in circumstances C, then he would freely perform action a,
then even God in His omnipotence cannot bring it about that S would refrain from a if he were placed in C.
This position leaves human freedom to operate outside of God’s sovereignty. That is, there are some things that God cannot do. The will of the human sits outside of God’s control. Of course as the Deity of the universe God has the power to do what He wishes to any human at any time. But that is not the Molinist position. Craig stated it precisely that God’s “omnipotence cannot” do certain things. That phrase seems to define omnipotence out of existence in any functional sense. He has the principle of omnipotence in place but does not allow it to operate. This is a contradiction; it is not a paradox.
Were Dr. Craig to suggest that God allows for a time the human will to operate with apparent independence so that the choice of salvation might be accomplished, then we might have a certain amount of commonality. The human being living a seemingly free life (though God has predestined the circumstance of life) will never the less choose according to the eschatology that God has set in place.
One of the characteristics of Molinist theology is that was developed as a counter-Reformation set of ideas. Many in the Roman ecclesial tradition were troubled by the strong sense of election that came from Luther and Calvin. The appearance of being mechanical drives many away from the theology of the Reformation as they seek a solution which accomplishes more thoroughly a place for human free will within God’s sovereign plan.
This position presents some problems. Craig also says that “It is, for example, God’s absolute intention that no creature should sin and that all should reach beatitude. But it is not within the scope of God’s power to control what free creatures would do if placed in any set of circumstances.” The first is logical and the second is theological.
The first is to ask, following the first criticism, why an omnipotent deity would not be free to control all of the created order? Dr. Craig answers this in response to another question.
How do you know that God couldn’t put together a world in which the unreached are people who wouldn’t bend the knee under any circumstances? In fact, this hypothesis has real implications for other issues like the wider problem of evil. For example, maybe only in a world involving scads of natural and moral evil could God arrange the sort of world we’re envisioning. Maybe His desire to achieve an optimal balance between saved and lost overrides the benefits of a world with less natural and moral evil. It may well be that getting the right counterfactuals of creaturely freedom in place to achieve (3) involves putting up with a lot of otherwise gratuitous evil. 
The issue becomes clearer in the middle of the paragraph by suggesting that God is perhaps working to create and maintain some sort of “optimal balance between saved and lost” and that there might be benefits over a world which could contain less sin and consequence from the fall.
I suggested plainly that this is more a logical problem than a theological one. It is clearly theological. The logical problem has to do with what looks to be the invention of scenarios to fill the argument’s lack. Dependence on “maybe” statements with neither an appeal to any exegetical material nor an appeal to a systematic having an exegetical foundation should leave the reader wondering whether this type of analysis is adequately fruitful.
The theological issue goes to the Lord’s position on sin and evil. Is God the sustainer of evil, enjoying its presence as it provides some sort of balance in the world? There are so many things wrong with this position that a book could be written. I will leave it to you to consider the consequences of God not being always in opposition to sin and evil.
Finally this from the same post:
But my suggestion is that God, being so merciful and not wanting anyone to be damned, so providentially orders the world that anyone who would embrace the Gospel if he were to hear it will not be placed in circumstances in which he fails to hear it and is lost. Only in the case of someone who would be saved through his response to general revelation would a person who would freely respond to special revelation, if he heard it, find himself in circumstances where he doesn’t hear it.
What he is saying is that condemnation is something that God is working to avoid. That is why he supposedly ordered the world as He did. That’s wrong. Condemnation is fully in His control. Suggestions otherwise miss the point of sovereignty. This allusion to II Peter 3:9 over-emphasizes the patience of God that Peter clearly expresses. But it misses the contrast against certain judgment, the inescapable eschatology of all who are lost. The passage is not about opportunity but about judgment for the mockers. God does not have to work around judgment by ordering the world in one way or another.
His suggestion of salvation through general revelation comes, at least commonly, from a misinterpretation of Romans 1. Romans 1 covers the lostness of the gentile world and Romans 2 the lostness of the Jewish world. In the end all are lost. But Molinists like to appeal to Romans 1:20ff and suggest that another choice was available to the lost, that they knew of God specifically and did not respond to the knowledge that they possessed.
Faith gets reduced to choice. Of course the definition of some in Reformed circles is that faith is the equivalent of knowledge. Both are inadequate. I understand the desire of the Molinist but cannot recommend it as a solution to the question of faith and how God manages the world.
Of final note, I have a lot of respect for Dr. Craig. He is a great defender of the faith. But there are some areas where philosophy must give way to the constructs of exegetical theology and this is one.