Science has closed the gaps in our knowledge of the workings of the world. With each gap that is closed believers move the goal posts, claiming that their God is still active in the world. In effect, until science can close every single gap they will have reason to believe. That is, either science must show it's impossible for God to exist or they can believe despite the massive onslaught of science. Because of this science some of the more reasonable believers will say God is not to be found in the gaps, but instead he is the sustained of the world. Yet look at what they've done. Either they argue from the gaps of they don't. If they do, then they must continually move the goal posts, which means they were wrong in the past. Thus arguing from the gaps is an argument from ignorance. If they don't do this, then this universe looks indistinguishable from a universe without God in it at all.
To be honest I don't think Loftus realizes that the more questions Science answers the more questions get asked. There is not a single thing that we can completely exhaustively claim to have fully explained.
Unless we can prove we do not live in a Matrix, or are not dreaming right now, or are not some brains in a vat, then believers will opine we all have faith. And if they can get us to admit this then they drive a whole truckload of Christian assumptions through that small crevice. Can we prove any of these things are not the case? Then they have every bit of a right to believe the wildly improbable things they do about a triune god, an incarnation, transfiguration, resurrection, ascension, and final judgment. This is a huge non-sequitur. There is no parity here at all, even if we grant these things, which I've written on before.
The bottom line is, we assume a whole lot - things we can't prove. For example, how do we know the light has the same speed all over the universe in all inertial reference frames? We don't really know that but its seems probably true. Loftus' whole argument seems to hinge on him thinking that "a triune god, an incarnation, transfiguration, resurrection, ascension, and final judgment" are all improbable. However he has not proven that they are improbable. No one can. If something is designed and put into place - probability is a stupid thing to consider because probability has nothing to do with it. If Jesus' Resurrection was an predetermined and deliberate act than there is no possibility that it would not happen. Science is full of finding out that the improbable is not only just possible but necessarily true.
There are other things to say but I'll stop for now. Others can chime in with more examples. But just think if a banker told someone that he would probably bring financial ruin upon himself if he invested all his money in one particular stock. What would you think if this guy invested his money anyway because his banker could not prove he would bring financial ruin on himself? Think on this and you see exactly what believers continually do.
I think the investment analogy is flawed. The Christian message is not that if you accept Christ you will bring ruin on yourself. A better analogy is of a person being bankrupt and hopelessly in debt and deserving to spend the rest of their lives in jail given the amount they owe and can never pay back. Then that person gets the news that all they have to do is believe and trust the one they owe and they can get the debt washed away and lavished with untold wealth - more than they can imagine. That is the Gospel. The biggest facepalm of all is that Loftus does not understand what he rejects.
Debunking Christianity: Christians demand that I must show their faith is impossible before they will see that it is improbable.