3 month old HATES belly time?

Should I just let him fuss or what? He's getting a very bad flat spot on one side of his head from always sitting in his car seat/bouncer. He's not supposed to lay on his back because he has bad acid reflux. His pediatrician said the spot will straighten up on its own when he starts sitting up by himself and crawling, but it just seems so bad that I don't see how it could. He also can't hold himself up very long on his belly because he doesn't get much belly time since he's always fussy when I try it. And I can't put him on his tummy after he eats cause he throws up when I do that. Sometimes he wants to eat every 2 hours so that's why. Anyways, he's on his belly right now, but he's crying.. What to do?