Actually, Little Snitch saved me from the Flashback trojan. A blog I visited redirected me to a bogus site with the trojan; at the time, I didn't know what it was, but later I recognized the URL as a Flashback infection site. My Mac did not test positive for Flashback later, however. Why not? Because I was running Little Snitch, wanting to know who my software is reporting to and controlling what traffic I see. Similar reason to why I run browser extensions like Do Not Track Me.
The variant of Flashback I encountered self-destructed when it saw I ran Snitch, for good reason: hackers don't want anyone to catch on to what they're doing. If you run Snitch, then there's a good chance that you'll see the traffic, catch on, and blow the whistle. Ergo the self-destruct.
Yes, Snitch has a barrage of notifications you must sort out for the first few weeks. Once you are beyond that, however, you control what traffic is allowed and what is not, and any new notification is an alert that something new is happening. In short, yeah, it's troubling to be alert to invasions of privacy and dangers inherent to the net. But it's often worth the trouble. It's saved me a lot of pain so far.