Bedtime is a time of day when children are more likely than at other times to experience feelings of loss. This is particularly so when one of their parents is not available to them, and your son's behavior is likely indicative of his missing his father. It does not reflect anything negative about you. It's important not to engage in any drawn out discussion about this, because the task is to help him separate from the day and fall asleep. So be sure to establish a nice routine, including a story, and help your son feel secure with reasonable measures (e.g., a nightlight on, door partially open, hallway light on, having a stuffed animal, etc.) and then be firm about adhering to the routine.
So is it ok for me to put him in his room and leave as long as there is a gate up? He usually starts to cry when I leave- does he feel unsafe, or just does not want to go to bed, because I give him a nitelight a movie is on softly and he has his stuffed animal.