Could be that the smaller stations bought the rights to Limbaugh's show to try an improve ratings, but that wouldn't fit into the insane mind of David Brock.
In this case, no.
What happened is that iHeartMedia (the network that owns Rush's show) is paying Rush somewhere between $40 and $50 million per year to carry his show because of the deal they signed with him in 2008. Part of that they make up through direct national advertising, but that only covers a small portion of the fees. The rest comes from iHeart selling the rights to the show to the 600 or so stations that carry him. The rights are VERY expensive—it's into the hundreds of thousands of dollars for most of the bigger stations. Those stations have to make up the money for the rights fee by keeping ratings for the station high and selling lots of advertising. The problem is that the whole Sandra Fluke boycott had an indirect effect. It didn't hurt Limbaugh directly; he was able to find new advertisers fairly easily. But when the huge list of companies started growing that wouldn't advertise during Limbaugh, eventually it led to whole stations being blacklisted. Advertisers wouldn't buy time on a station if there was any chance that a barter ad could be heard during his show. So, with ad revenue crippled, stations couldn't make up the cost of keeping a guy who is several times more expensive than even a local host would charge. Thus, iHeart had to step into these markets and put the shows on their own stations, forgo the licensing fee, and try to make up for it by keeping whatever local advertising they could scrounge themselves.
In Indianapolis and Boston (this case), Limbaugh was on heritage AM news/talk stations owned by other companies. The new stations are ones that iHeart owns and operates. In Indianapolis, it's a sports-talk station. In Boston, he actually moved to this station for a couple years not too long ago, but it was a ratings failure. Actually, Rush has been getting "demoted" to these types of stations in New York and Los Angeles for a couple years, and the ratings are showing a major decline from market-leader to also-ran. Right now, he's barely hanging on to the title of most-listened-to radio show in America, just ahead of NPR's Morning Edition, and that estimate comes from Talkers Magazine (which promotes the format as a whole) so it might be inflated. So it's a double whammy: lost ratings means lost local advertising, and lost rights fees for carrying the show on their own stations. iHeartMedia is probably eating quite a bit of a loss as of late for the show.
Limbaugh's contract with iHeart ends next year, and so does his affiliation agreement with Cumulus, a big station owner (35 of his stations are owned by Cumulus). It's not out of the realm of possibility that come the end of next year, he finds himself out of a job.