Longer answer: Tooooo maaaaaake themmmmmm funnnnyyyyyyyy!
In all seriousness, the movies we riff on are bad. Very bad. And usually, they're bad for various reasons, including such boring filmmaking details as pacing, editing, overall coherence, or questionable taste levels.
Just like Mike, Kevin, and Bill did way back during the Mystery Science Theater days, we sometimes edit our digital video releases to increase their comedic value. That's to help you, the viewer, as well as to make the end result more entertaining — or, at least, watchable.
For example: if a movie includes objectionable scenes of extreme violence, sexual assault, gratuitous nudity, or something else that we think would detract from our viewers' ability to actually enjoy the riffing (by "taking you out of the movie" due to its awfulness), we will make edits where appropriate. The same holds true for very slow, very boring scenes: there are only so many jokes we can make about things like that, and so we think our removing bits like these from the movie is doing it - and the audience - a favor! (Fun fact: Rick Sloane admitted to us that our slightly-edited-for-pacing version of Hobgoblins was better than his original cut. He also made us "promise" not to "tell" anyone he "said" that. Your secret's safe with us, Rick!)
And while it may look like we sometimes delete several minutes' worth of footage out of a movie, the reality is that we typically make many smaller edits all throughout, so the vast majority of the movie remains intact — for better or worse. Some movies may warrant an extreme edit, but that is a rare exception.
We always take great care to ensure that the plot (or whatever passes for it) remains unaltered, while also making sure that the RiffTrax content you paid for is the funniest it can be.
Hopefully this helps clear up our reasoning and methodology. We strive to make it so that you don't notice the edits, and any missing movie is made up for by the added value of jokes. So please enjoy our much funnier versions of these classic (and not-so-classic) movies, won't you?