Sigh. He has two "arguments", here's his first:

So logically you have to have faith in both the belief in God and Science.

The difference is that your "faith" in science (here specifically, in the men who perform the science) can be tested - and this makes all the difference in the world.

Argument two is a hand-wavy assertion that pain (and god's allowance of it) is a result of god's imposition of free will. He's really just apologising for god's allowance of pain - an apology which is clearly unneeded if we assume there's no god.

He then goes on to say that this (somehow) shows that faith is logical.