It's because Congress hasn't appropriated any other funds to pay for it. Does your DMV give you a free driver's license every time you visit the office? If so, great, but that's because your state funded it (I've never lived in a state that did so).

Now, can you argue that the documents from PACER should be available to all citizens without cost on their part? Sure, but that's not what has happened up to this point, so until then someone has to pay for PACER.

TL;DR: Show them the money. You'll get what you want.