We didn't have this exact problem, but here are a few suggestions that have worked for us, or I've heard from others:
1. Put an article of clothing of yours in the crate with him. Your scent should help relax him and make him feel more comfortable. I was literally putting my undershirt in with our dog... note - you may lose a shirt of two!
2. Try conditioning him so that going in and out of the crate is no big deal. Teach him the command "crate" and give him a treat for going in the crate before you close the door, and then another treat after you close the door. Maybe for an hour a night, 10 minutes on 10 minutes off. Just keep doing it over and over. At first you may need to give his butt a push to get him in, but after awhile he should start going in and out on his own.
3. Put something in there to keep him occupied. BE CAREFUL. It's not a good idea to use a bone that's small enough for him to choke on, so it's got to be really big and something he can't break into pieces. Lots of people put a KONG with peanut butter in it in the freezer.
4. Finally, we always take our guy for a long morning walk, then feed him, let him out to pee before we go, then crate him. Generally the walk tires him out and then when his belly is full he just wants to sleep. Not sure if this will work the same way with a puppy, but as they get older it's works great.
Generally I'd just recommend you spend as much time with him in/around the crate when you're home so he thinks of it as one of the regular places he likes to go. If you have to you can even crawl in there and have him follow you, hang out for awhile... whatever it takes to get the job done.