I have had experience with this since my son was about 7. He is 11 now. He progressed a long way since then, but your son may not go down the girly route. I started out doing my son's hair in the way that you did, starting with a low ponytail. When his hair gets longer, a good style is a single braid. It is very practical, looks great, and keeps all the hair together. If not, try a low bun. Both are not too attention attracting. What might help you to deal with the girl comments, is spreading news about famous guys with long hair, or just get your son to know about them. Just look them up. Also, try not to draw attention to his hair, and tell this to your son too. But if it does, do not make a big deal about it when it first happens, the other children only want a reaction. Now, of course, nothing stops anything completely, so you may want to get teachers notified of any problems, as they can deal with it first hand. If you have any other questions, please ask.
Daisy :)