Well, this isn't exactly right. If a company licenses a property, they're still making money off of it. For example, take Buffy. For years there were licensed comics (and I think some tie-in novels). They weren't canon, but money still was passed to the IP owners (Fox, Whedon, etc), depending upon the licensing contract.
Years later, the show is long over, and they decide to run a series of comics that ARE canon. Of course it contradicts the others (for that matter, the tv show often did), and since many of the original folks were involved in writing, I'm sure they got a bigger slice of the pie, but they're doing new work, so they should. But that doesn't mean that there was no pie before, and getting pie is not the only reason to declare one work canon while another is not.
I believe canon is not about making more money, but about telling a story with intent beyond a single work. It can be handled well, and it can be handled poorly (or hell, not at all, with the Doctor Who example), but it can be important, depending on what you're trying to do with an idea/universe/etc. I dislike the concept of headcanon too, but that's a rant for another day!
If it was purely greed driven, why not take a slice of the licensing, do zero work, and let the cash trickle in, not caring if it's canon or not. Money for nothing (well, for previous work, but still, overhead at that point is effectively 0)! The only way you would NOT make money is if the work was in the public domain, which is more or a free-for-all as far as the narrative is concerned. In that case it makes sense to contain your canon a little bit. Say you and I are writing Alice in Wonderland stories. I want the Mad Hatter to be a bus driver, and you want to kill him off. Your third story would be so far removed from my third story, so the audience would need to know what history the current events reflect.