See Senator Lieberman's 2010 letter to Senate Appropriators for clarification (which I've updated my essay to reference):
"As you know, Court documents are electronically disseminated through the PACER system, which charges $.08-a-page for access. While charging for access was previously required, Section 205(e) of the E-Government Act changed a provision of the Judicial Appropriation Act of 2002 (28 U.S.C. 1913 note) so that courts “may, only to the extent necessary” (instead of “shall”) charge fees “for access to information available through automatic data processing equipment.” The Committee report stated: “[t]he Committee intends to encourage the Judicial Conference to move from a fee structure in which electronic docketing systems are supported primarily by user fees to a fee structure in which this information is freely available to the greatest extent possible… Pursuant to existing law, users of PACER are charged fees that are higher than the marginal cost of disseminating the information.”
Since the passage of the E-Government Act, the vision of having information “freely available to the greatest extent possible” is far from being met, despite the technological innovations that should have led to reduced costs in the past eight years. In fact, cost for these documents has gone up, from $.07 to $.08-per-page. The Judiciary has attempted to mitigate the shortcomings of the current fee approach in a variety of ways, including limiting charges to $2.40-per-document and the recent announcement that any charges less than $10-per-quarter will be waived. While these efforts should be commended, I continue to have concerns that these steps will not dramatically increase public access as long as the pay-per-access model continues."
Keep in mind that the US court system is not funded through filing fees. Courts generally have struggled with funding. Minimum mandatory penalties and the drug wars caused Miami to end up with four downtown federal courthouses and a (relatively) new federal prison. These facilities were not inexpensive.
To get back to the principal issue, the Government gets free access to PACER (and even free photocopies at the courthouse) whereas a private defendant, like Swartz, has to pay for these out of his own pocket. The government gets a case agent, the defendant gets none. The defendant may get a public defender, but only after he has exhausted his funds--and this happens.