Science and my own Reason have been obstacles to my Faith as well because when I think about all the incredible stuff that the Bible says Jesus did like perform miracles or rise from the dead I find myself doubting that because it seems impossible. Also, Science doesn't seem to be able to prove many things from the Old Testament either, true that most of those stories could just be parables or stories made to get a certain idea across, it still leaves me wondering. Materialism then comes into play and I agree with that a lot: if God exists, where is the proof? if there is a Heaven and Hell, where are they?
Finally, overall fear is a big challenge to my Faith. I often think about the possibility of there being no God or heaven and that after we die we are gone forever, lost in oblivion. Or the chance of their being a God, but not the God I believe in, and because I did not worship that god when I was here on Earth they'll want vengence and I'll be damned for eternity. Then I worry about not pleasing the God I believe in now and always screwing up and then having to pay for all of that after I die.