I have seen multiple potential explanations for the targeting:

1. Flynn was likely to help Trump torpedo the Iranian deal (which Trump did anyway)
2. Flynn is an intel pro and would have quickly figured out what Brennan and pals were up to un 2015 and 2016 with respect to spying on the Trump campaign (the onion is still be pealed back daily on those issues)
3. As you suggest above, Flynn knows the bad actors in DC and would be particularly effective in rooting them out. Here's to hoping he still gets his chance.