It's likely the government doesn't like him because a few years ago he released 18 million pages of public court records that the government ordinarily charges 8 cents per page to access.[1] As these were public records, what he did was not illegal nor, in my opinion, immoral. But the government didn't like being undercut, and now they have a good opportunity for some payback.
I'm pretty confident all the data in PACER will be made public at no cost at some point in time. I think the $.08/page charge is supposed to cover the administrative costs (like paying for photocopies) but the PACER program actually runs at a surplus. I think this may have even been part of the rationale for the trial they ran which Swartz used to do the downloads. The government wants to open up PACER.
But what struck me as partularly stupid about what Swartz did (besides the fact that the data will probably be released anyway, in due course, without the need for "activism") is that he installed stealth code on a computer in a Federal Court Law Library. Of all places he chose a federal building, and a Federal Court Law Library. This just sounds idiotic.
And the irony of it all, at least to me, is I just downloaded his Superceded Indictment for free from archive.org. It appears others are succeeding in making court documents publicly available without installing stealth code on federally-owned computers. Maybe they do not have everything in PACER yet, but I think it's only a matter of time. Courts are perhaps a little slow to change with new technology but despite their budget constraints they are definitely making progress. And publicresource.org seems to be getting bulk data with the blessing of the courts and without installing any stealth scripts on Law Library computers.
If one really wanted to engage in some sort of activism to free up (what should be free) legal documents, maybe a better focus is Lexis-Nexis. A true monopoly, founded on a dubious intepretation of copyright law. Can you copyright court decisions? They managed to do it. And the founder is on the Forbes list.
PACER is partially open now; for example, I went looking a little while ago for filings relate to modafinil prosecutions, and wound up paying nothing at all because I fell below their $10/monthly cap or whatever.
See http://blog.simplejustice.us/2011/07/20/swartz-caught-in-a-c... for some analysis from someone who doesn't support what Swartz did, but nevertheless sees this as a vindictive prosecution.
[1] http://www.wired.com/threatlevel/2009/10/swartz-fbi