I've been in animation (mainly 2D) for over 15 years and I can't count the number of times people have asked me to "go into business" with them. I can't count the number of studios (in NYC alone) which have gone "belly up" because the people in charge (talented though they may have been) simply did not know how to run a business!
If you're a newbie, the best you can hope for is to TEAM UP with several others of like mind who know not only the software but who have basic business skills. And yes, unless you are the guy with the geets ($$$$), you're definitely better off learning the software and working your way up.
If you're "running a company", about 105% of your time is going to be spent on the phone trying to drum up work and humoring clients.
I HIGHLY recommend the book "Animation from Script to Screen" by the late Shamus Culhane. Though it was written with the traditional animation studio in mind, the lessons apply to ANY animation studio. He spends a great deal of the book talking about the intricacies of running a studio. It isn't a substitute for business smarts, but it IS worth a read if you have even the slightest inkling of what it's like to run a studio (Culhane ran his own shop from the 1950s until he retired c. 1980).
Good luck and happy learning!
"Ad astra per aspera..."