"Most" encoders overall definitely use mkv nowadays. You know, all those evil people not adhering to your world view, they tip the scales against your favor.
Even if you reduce your view purely to the "normal" fansub world, MKV still has the slight numerical advantage over MP4. If you don't believe this, run some checks on evul evul places. Heck, even on Animesuki itself, you'll find more groups listed with mkv right now
The thing is, I'm not even that much opposed to it. For normal hardsubs based on TV captures, MP4 is a perfectly valid choice - especially for those groups who don't want to have their scripts demuxable. Nothing wrong with that. As long as it's clear WHY it was chosen. And I'll tell you a secret, it's not because of your bigotry