I also agree that this is not something to go to the ER about, especially not 3 times. If your pediatrician says that it is not a hemorrhoid then it's not! Bleeding and the skin flap are most likely caused by hard stool and straining. The straining and hard stool cause small cuts called fissures. Try adding some prune juice to his formula or just feed him a small amount, 2 oz, of prune juice to help soften his stool. You can also put a little vaseline on a cu-tip and rub a little around his anus to help ease the discomfort.
If your pediatrician didn't explain this to you then I would consider getting a different pediatrician. Your pediatrician should also be able to give you additional advice on how to relieve this problem.