I answered another post a week ago from another mom who has a son who is 3 and a half having trouble at night.. This is the age, when they really have become aware of what is going on around them.. Their imaginations are very real to them.. Here is what I suggest.
He sounds extremely bright. This is why he is so scared.. His imagination is so brilliant he is freaking himself out.
If you all are religous, when you say your prayers at night emphasize that he is praying to be watched over and loved by God.
I would get him a sound machine for his room. This will help block out the sounds in and around the house. (If your son balks, hide the machine and turn it on BEFORE he goes to his room at night)
Also make sure he has his own flashlight. Our daughter went through a stage of being afraid of shadows.. Even during the day. So we gave her a flashlight and she learned very quickly, there was never anything there.. she also learned SHE was making shadows with her own flashlight. We made sure each night it was next to her in bed.
We also had "dream coins". To you and me they looked like quarters, but to her they were "talisman" to help protect her from any bad dreams or scary thoughts. Placed under her pillow, they were always protecting her.
One morning I noticed a pile of coins under her pillow, I asked her why there were so many under her pillow.. She said she had a really, really bad dream!
Another mom here on mamapedia says they have "Monster spray". It is a small squirt bottle filled with water.. When sprayed in all corners of the room or under the bed, it keeps all monsters away from the child.
Maybe instead of you going to your child's room, have your child come into your room and sleep on a blanket on your floor next to the bed.. This will not last long, they get tired of the floor..