I agree with Emily, sometimes you can get other infections from antibiotics... my daughter got a bladder infection from the antibiotics for her ear infection. So taking her to the doc might not be a bad thing. They can test for other infections to see it that is why she is hurting and treat her for them if she has any.
Also, give her a few warm baths, make sure she is sitting in the water... at 2 mine like to stand & play more then sit. But if they could have they would have taken baths all day & sometimes we would give them a few extras just because there was nothing else to do. Baths never hurt - they can actually be fun.
Also, has her poopoo changed any??? Is it harder then it use to be?? Sometimes if it's hard for them to do it does hurt & can cause little cuts or cracks - but we can't see anything wrong. When my little guy has issues I give him an extra cut or two of juice a day to help the flow so to speak and also use vasiline on him in that area so that it will help to lube it when it is coming out, plus it protects the area from extra moister (which helps the cuts/crack/tears to heal). Sorry don't mean to be gross, but I don't know how else to put it. Usually in a few days he is back to normal & no more crying when he is going or being cleaned up.
Also, maybe for a few day just a warm wash cloth instead of wipes... wipes have things in them that cause little cuts to sting when the liquid on them get into them. Warm wash cloths is just water - which means the little cuts or cracks won't sting if they are there, plus warmth sooths things a little more.
I hope your daughter gets to feeling better & that some of my tips are helpful. Take care!!!