That's the feeling I got with the cancellation of Spectacular Spider-Man too - it's too much of a coincidence that they both were canceled at the same time, several months after Disney took charge. It's a shame too, because both shows were heading in the right direction and were pretty well-received from the fans. Hopefully Disney knows what they're doing and some good will come out of this all.
Well, with SPECTACULAR SPIDER-MAN it was more complicated. Ultimately after about a year of haggling it was determined that Sony owned the show and it was up to them to continue it or not. As it had been out of production a year at that point, it was unlikely they would continue it without Marvel's blessing. As Marvel/Disney now has the exclusive TV rights to any Spider-Man cartoon that ISN'T SPECTACULAR SPIDER-MAN, they went to make their own, hence, ULTIMATE SPIDER-MAN.
As for WOLVERINE AND THE X-MEN, that's trickier. The DVD's of the show are released by Lion's Gate but I don't think this show is attached to anything Fox is doing with the films. As Disney is in control of quite a few shows and knows how to harness a cheaply produced show into a mega hit (see HANNA MONTANNA), I think they are having more of a say on Marvel's TV arm than anything else. Thus, maybe they wanted to prioritize Marvel's TV animation budgets to making AVENGERS: EARTH'S MIGHTIEST HEROES (and possibly that THOR cartoon we have heard of, but that is still a rumor), as well as second seasons of IRON MAN: ARMORED ADVENTURES (due to the success of the films) and SUPER HERO SQUAD, with "their" Spidey cartoon in the wings. Maybe 4 cartoons in some stage of development/airing was the max they wanted to shell out for; Disney "bought" Marvel and they have ultimate say in how that "investment" is spent (although one imagines Disney cares more about merch, TV, and film and doesn't really bother with the comics). Perhaps Disney felt that if they could only afford or allow work on 4 cartoons, they would choose the ones where they see current film efforts shifting. Only two months ago, "X-MEN: FIRST CLASS" as a film was still mostly rumor. Now...it is limping into pre-production.
It may be possible that Disney saw an X-Men cartoon at this time as somehow giving "undue advertising" to the Fox films, of which Disney sees zero profit. It may also be they saw no need to continue a cartoon that, let's be honest, came about due to the hype of "X-MEN ORIGINS: WOLVERINE", which was hardly the studly box office beast that IRON MAN films are. It could be some combination of all three explanations. Still, I imagine once Fox gets into gear about FIRST CLASS, some X-Men cartoon that is similar will be inevitable.
I would also assume that any DTV deal with Lion's Gate will not be renewed. Disney (or a sister company) can print out animated DVD's.
There's a saying, which Spider-Man once quoted when he teamed with Venom for the first time against Carnage, that fits: "When you make a deal with the devil, you have to learn to jump around the flames." In exchange for financial stability in a rough economy, Disney commands Marvel, not the other way around. This can bring forth good things, or bad, but what it does bring about is there is a "ONE ABOVE ALL" that Marvel has to tow the line for. And one casualty may have been WOLVERINE AND THE X-MEN, but no one will admit that...at least not while they still have their checks paid by Marvel/Disney. Maybe in 15 years when someone retires, it will make a nice "didja know" for some Internet site interview.