With the exam turning up nothing, it could just be constipation or something simple that a 3 year old can't explain or express....if she is crying or actually seems like she is in pain, then I would be more concerned....but if she is just saying her butt hurts, then it could be anything - maybe scratchy toilet paper, elastic on her underwear, sitting too long making her tailbone sore, etc etc...3 year olds may just want you to pay attention to what they are saying and 'make it all better'' by using a 'magic cream' or something...
But - you may also want to check her sheets, etc at night - a neighbor of mine had a son with pin worms. This can make her butt hurt but show no signs except at night (but I would assume the doctor would be able to catch this...?). Good luck - good news is she can't stay 3 forever and eventually she will be able to tell you what the problem really is....but hopefully she won't have to at that point - it will have already fixed itself...