Perhaps your child does not like something about his bed, such as the way it feels, or the way it is positioned.  Try to rearrange the bed, make bedtime a pleasant routine (bath, baby massage in the bed, and then reading a book), and definitely have a night light on to make night-time less scary.  Does your child like a particular toy or baby blanket?  Make that a transition object that your son takes to bed for comfort.  When he wakes up at night, reassure him and gently soothe him back to sleep.