First off, the call letters for Channel 30 in St. Louis were (and are) KDNL, not KNDL. If you're going to complain, get the facts straight first.
Next, it's true that KNLC has always been a primarily religious station, but they've always had secular, general-entertainment programs thrown into the mix as well. In addition to syndicated cartoons over the years like Captain N, KNLC was briefly the home of the Fox Kids Network in the mid-1990s, has aired many a Western in its time, and even carried rerums of Frasier this past year.
Why didn't Captain N air over KPLR or KDNL? Who knows? Most likely, neither station had room to air it and showed no interest in buying the show. KNLC was the only other option in St. Louis at the time. If television schedules from 20 years ago make you physically uncomfortable, you may need stronger help than we message board denizens can provide.