One thing that's crucial to helping your dog be comfortable in his crate is to pre-condition him to being there. This means getting him to go in a number of times for short periods, then letting him out and rewarding him for being good about it.
Of course, once you manage to get him into the crate, it's essential that you strictly maintain some discipline. Never let him out when he asks, such as whining or barking. It's not easy, but you must ignore those behaviors, or he'll think that's how to get your attention and get his way.
However, if he starts whining after he's been in there a while, it could be a sign that he needs to go outside for a moment to eliminate. This behavior does need to be rewarded, at least by recognizing what it means. Just try to let him out between whining, or he still may associate the whining with getting out.
At night, it may help to cover the crate, as it may help him to feel secure, not to mention, diminishing the light in there, so he can settle down and get to sleep.
Never use the crate as punishment, however. You don't want him to associate it with anything negative, or it will become increasingly difficult to get him to use it. And if you love your pup, you don't want him to be miserable, either.
As long as he feels secure, happy and comfortable in there, his crate will become his refuge and personal hideaway.