Children would rather be sleeping, if they can. Waking up is not something they actively choose to do. But it's lonely lying in your room in the dark, unable to sleep, with thoughts or insecure feelings running through your mind. I remember many, many nights as a young child being afraid to bother my mommy, who was stringent about such things, but feeling lonely and miserable. I've never been a good sleeper.
I've known lots of parents who have allowed a child to sleep in their room, perhaps on the floor by the parent's bed, when they awake at night, without causing a bad habit. Your son will sleep through the night again when he is able, and would prefer to do that now, if he could.
You could try a reward system to see whether he can choose to stay in his bed. If he tends to come to you, say, 6 times in one night, put 6 sections of a straw, marbles, or other symbolic item in a cup. Tell him that each time he comes in your room, you'll take one item out of the cup. But if he stays in bed, he will still have some items left in the morning, and for each one, he will get a prize (if you can think of a healthy treat or fun privilege he likes, that would be ideal). OR, if he has X items left in the cup, he will get a reward, such as one-on-one mommy time, a special breakfast or special project. You can handle this different ways, but rewards should be almost immediate for this to work.
Another thing to check is to make sure his room is as free as possible of chemicals, especially air fresheners, fabric softeners and scented detergents. These contain some harsh ingredients that are known to be central nervous system irritants, and can cause seriously disordered sleep. Some food colors and preservatives also excite a child's nervous system and can disturb sleep. So the cleaner and more natural, the better, for him AND for you. And television within two hours of bedtime can also disrupt his production of melatonin, the natural sleep-inducing hormone that's made in the brain at night.
