I would hope Musk's position is rooted in the knowledge that we need to get off of fossil fuels in a few decades or we're done. If hydrogen as a non-thrust fuel has any use, it has so much research ahead of it; there isn't enough time for that.

This is mainly driven home by the idea that hydrogen is very much in abundance in the universe, but here on earth it really only exists as hydrocarbons. Hydrocarbons are a tricky thing to exploit without contributing to global warming.