I think that's a very suspect use of "natural". Of course, many uses of "natural" are suspect, in that people smuggle all sorts of their personal prejudices into it. E.g., the way a number the Civil War declarations of secession mentioned how it was natural that whites should rule over blacks. Or the way today that religious conservatives think that the natural order is the dominance of men over women, and that gay people are unnatural.
Even in this case though, I don't think it means anything more than "we were so used to using our monopoly power to steamroll everybody that we expected to keep on doing that". Microsoft only ever dominated the personal desktop computer OS market. They were a minority player in server OSes their whole existence, losing first to big iron and later to Linux. The handheld market went from being owned by companies like Palm to Apple and Google dominating. I know less about the embedded market, but Microsoft has been trying to own that for 20 years, and I don't think they've ever had a dominant position. I think even their desktop OS dominance was less to do with Windows being an amazing operating system and more to do with it being the thing that ran Word, Excel, and other popular business software.
So I think tsunamifury is right. Gates got so comfortable winning he saw it as "natural", rather than a combination of luck and their willingness to be an aggressive monopolist in a newfangled industry and during a period where antitrust enforcement was falling out of vogue.