I think more people would have known him as one of the major stars in ROH as opposed to 'that jobber that hung around with Raven in TNA' prior to signing with WWE as TNA weren't exactly the internationally known brand they are now in 2004. Regardless of that though, as far as I'm aware, WWE wrestlers aren't contracted as direct employees, but rather 3rd party contractors (or whatever the American variable is, that's why there has always been rumblings about not having an official wrestelers union, etc) which gives WWE certain benefits, with that in mind, as CM Punk created the name he alone is entitled to ownership of the name.
Also, it's pretty rare for WWE to continue to push anyone to the level Punk has been unless they work their ass off and have the talent to back it up, so although they may have given him the mic time and titles, it's because he's worked his ass off to deserve it under the name that he himself created.
If you're working with someone as a third party, they have no right to ownership over your products or services unless you explicitly say otherwise (wouldn't have thought it'll be wholly different to that in America). I can understand what you're saying about WWE looking out for their best interests (it wasn't me that said they were assholes or whatever the insult was, just backed up Punks case) but it's Punks image that is associated with the name, not the WWE logo, therefore he's got to look out for his own best interests and not giving them ownership of his name is definitely in his best interests.