"Geared towards colonization" sounds a tad thin if it entails adding some shuttlebays but also quite a bit of firepower. Perhaps "geared towards planetary assault" might be more like it?
That's what I'd think. The military probably wouldn't be too interested in shipping around civilian colonies; a lot of them aren't even necessarily Federation to start with. Starfleet, of course, has an interest in protecting most everybody from everything (as long as it doesn't violate the prime directive
), so there's that.
But what would any military (de facto or official) want with fast, armed transports? Delivering stuff in dangerous situations, of course. Like a planetary assault - which Starfleet would do, if they had to drive out the Klingons or whomever. And if you can't reliably use transporters for whatever reason, you gotta have lots of shuttles, preferably in lots of bays so there's less of a bottleneck.