The runners are messengers, not terrorists. Aside from other sources, Jacknife specifically states that Project Icarus was designed to take out the messengers and disrupt the lines of communication. What the people they're delivering these messages to are doing, however, is never mentioned.
Some important things to note here is that most of the situation in the game is the current mayor's fault. Prior to him, police didn't give a shit about the runners. If you remember, in the beginning of the game, the characters are very confused as to why people are suddenly shooting at them. This is because those aren't policemen. They're members of the Private Security firm, Pirandello/Kruger, specifically sent to kill the runners. So, we can infer here that the runners were mostly harmless. This mayor is trying to crush all possible opposition, whatever it may be.
Also, well, the government isn't all that great. Here's something directly from TvTropes:
If You Can Read This: A naive Innocent Bystander is Tempting Fate when he types that he pities the Sinister Surveillance who has to monitor his porn surfing. He offhandedly wondered what they'd do if they learned he was quitting his job; tie him to a chair and beat him bloody? Guess what? That's exactly what they do!
Plus, there's that whole "November Riots" thing....
