There could be a lot of things going on-
~ She might not be well lubricated. If she is nervous or scared, and not really into sex because she is nervous, her vagina might be really dry and that would hurt alot. You can fix this by increasing foreplay (like at least 15 minutes of foreplay for her, oral or fingering or whatever) so she is really relaxed and ready for sex. Or use a store bought lubricant along with foreplay, it will really help.
~ You might be going in really deep and hitting her cervix, that hurts some girls. If it seems like that is the case, let her control the depth of penetration for what feels good for her. Try different positions that don't allow for so much depth.
~ She might be scared and clenching her vaginal muscles. That would hurt to. Try to get her relax like I said above.
~ She could (though unlikely) have some sort of infection or medical problem that causes it to hurt.
~ She might (though unlikely) still have had a hymen, in which case it might (though unlikely) have hurt when it was broken.
What are you using for protection? Also, she needs to be seeing a gynocologist now that she is sexually active.