If your son has been in kindergarten since last fall and is still as miserable as you describe, there is a problem. Is your impression of his misery based on what he is telling you or on reports from the teacher? Ask the school counselor to observe your son in the classroom so that you can get an objective opinion of what is going on there. Some children believe that mom wants to hear how much they missed her, so they tell mom how sad they were all day even though that was not the case. It could also be that your son feels threatened by some of the other children and so doesn't feel safe in the classroom. The counselor's observation can help you know if either of these situations exists.
Since this problem has apparently been going on for awhile, you will probably want to get some counseling for you and your son. The school counselor or your pediatrician can refer you to a therapist in your community. In the meantime, be very matter-of-fact with your son. When you put him to bed each night go over the schedule for the next day in detail ("I'll wake you, you'll dress and brush your teeth, ..." etc., right through going to school and through the school day, to "Then I'll pick you up and we'll come home and you'll play until time for supper ..."). Routine is very reassuring to children, especially when they may not feel totally confident about a situation. Going over the daily schedule in detail can help your son to feel better about the day.
Make sure that your son knows that you have confidence that he is safe and that he will be fine at school without you. It's usually easier to separate from mom at home, so let him ride the bus to school or ride with a neighbor. Ask the school counselor to help with some support while your son is at school, checking on him during the day as needed.