We currently don't have a rename function. This is something we are investigating for a future release. One way you might accomplish this now is to use the iTunes functionality to transer pdfs to/from reader. That would be a bit of a hassle, but if you have specific files you use a lot it might be worth it. I have a post in this thread describing how to use itunes to move files to the iPad:
One other note: Many users find that simply upgrading to iOS 5 from iOS 4 is enough to get better PDF names. In iOS 4, the system would rename files if they were opened from Safari or Mail. That is improved in iOS 5.
Finally, renaming is a feature we'd like to add in the future. Thanks for your request and please keep watching as we improve the app!