We're not REALLY bad against the run. Matter of fact, we had a pretty good run defense, which took a big blow when Jason Ferguson went down.
I remember us being "Colts run D of 2006" bad for long stretches, even before Ferguson went down. For some reason, teams just haven't run as much against us. It also helps that our own offense usually manages to keep the ball for long periods of time (often doing nothing with it).
EDIT: Looking up some numbers, we're among the WORST in the league in stopping runs behind either offensive tackle. Average up the middle and to our right, very good to our left. Jacksonville are, by a SOLID margin, a "run up the middle team". 77% of their runs are guard/center. Only 1 other team is above 70% (SF) and less than a handful more above 60%. For the few runs they have had to the sides, they've been very good left end, decent left tackle (gonna be a problem) and about average to the right. It's going to be VERY interesting to see if Jacksonville call a lot of "up-the-gut" runs or if they'll game plan to exploit our weakness.