I guess I don't see the difficulty in funding it via taxes, like the court system in general. To run a court system, we need to maintain buildings, pay judges' salaries, pay public defenders' salaries, pay bailiffs' salaries, store paper documents, hire stenographers, hire janitorial staff, and all sorts of other things. In the 21st century, storing and making available some PDFs is just another routine part of a functioning, transparent court system, and not even one of the more expensive parts.
We can't even fund things we all agree that we need via taxes at this point, like paying down the national debt. Right now the government budget is zero-sum, and this has been true for some years now.
If you want something you get rid of something else, and while I'm sure there's many things we could find to pay for PACER from appropriated funds, the problem is getting enough of Congress to agree on that, and getting Congress to take the issue up at all (because given that PACER is already funded, changing the funding source really isn't a very important issue for them).
