I agree that punishing him for crying because he has to play in his room makes no sense . . . it seems playing in his room is already the punishment. This is an issue in which you as a parent need to change your thinking, in my opinion. Kids like interaction and even at five, they like to be around parents and family. Last summer when my oldest was 5 and my youngest 4, I had quiet time every day. They did go to their rooms but they were ready because we had been swimming all morning and early afternoon, at the park, at the museum. They'd had lots of energy outlets and were tired. My 4 year old would fall asleep (the plan) and my 5 year old would play dress up and with his toys. But they both had no problems with it and liked the hour in their room. If he had cried . . . I'd not have made my 5 year old do it. Then the "in the room" time turns into a punishment. It wasn't meant that way.
good luck
Maybe he just wants to be with you. Are you sending him to his room as punishment, or just because you need to get something done? (I wouldn't want to go to my room either if I felt like I was being sent away because I was undesirable.) I agree with Sandman that you are hopefully not making him stay in there for hours. Are all his toys there? If you want him to spend time there, they probably all should be. You should spend some time in his room with him as well, if his problem is that he is lonely there.
(By the time he's a teenager, you'll be wondering why you never see him because he's always in his room.)
Its pretty simple, he doesn't want to go into his room and reacts in the only way he knows how. You either need to make his room more attractive to him, or maybe limit the time he has to play in his room. But essentially, you ignore his crying. Hopefully, you are not making him stay in his room for hours.