Maybe it has to do with the length of the animated feature. Seems to me that DC caps their animated movies at a hour & twenty minutes, maybe a hour & a half. Ya get a family of four - parents & two kids - into the theater, they've shelled out thirty-five to forty to be there, for not very long at all.
First off, direct-to-DVD movies are limited to c. 70 minutes for budgetary reasons -- given the projected DVD sales and rental income, a longer movie would cost too much to be profitable. So that would have no bearing on the potential length of an animated theatrical feature.
However, plenty of animated feature films are, in fact, between 70 and 90 minutes. To pick some Disney films,
Alice in Wonderland was 75 minutes,
Snow White was 84 minutes,
Pocahontas was 81 minutes,
Aladdin was 90 minutes, and
Dumbo was only 63 minutes. The three
Toy Story films were 81, 92, and 103 minutes (each exactly 11 minutes longer than the last!). The two
Kung Fu Panda films were 88 and 90 minutes.
The Incredibles was actually fairly long at 115 minutes, but
Megamind is 96.
So clearly, a running length less than 90 minutes won't keep an animated film from succeeding in theaters. It's just not a factor. In fact, theater operators love shorter movies because it lets them show the films more times in a day and thus sell more tickets.
And since DC's animated films are now known as direct to DVD, it'll be an even harder sell for 'em to get folks into theaters.
Marvel's animated efforts pretty much suck, so they'll stick with the live action, for sure.
Again, there's a difference between theatrical and home-video movies that you're failing to take into account. Presumably a theatrical feature would have more expensive, higher-quality animation, a full orchestral score instead of synth, and generally better production values all around than a direct-to-video feature, creating more of an incentive to see it in the theater. Look at the difference between, say, Disney's lavish theatrical features and their cheaper home-video sequels. Marvel's DVD movies are made for a certain budget that's commensurate with the potential profits from that market. If they did choose to make a theatrical feature instead, that's potentially a more lucrative market as well as a much higher-profile one, so they'd put more money and care into it. And so would Warner Bros/DC. Their DVD movies are pretty high-quality for that market, but if they did a theatrical feature, it'd be another level above that.