Oh I crated Hobbs until he was 100% potty trained and I am still currently crating Hootie because she is only 16 weeks old and not potty trained yet. They both would yell and scream when I put them in their crates. They both ended up getting used to them, though. Hootie doesn't cry anymore when I put her in there. One thing that really helped for us is every morning I put my t-shirt that I slept in Hootie's crate. She can smell me the whole time I'm gone so it really helps with the separation anxiety. Don't worry...your little guy is not being hurt. He is just being spoiled!
He will definately get used to his crate in no time and actually learn to love it!
If you take him out of the crate when he cries, he will ALWAYS cry...so try not to do that. Just ignore him, if possible.