Don't worry. If Linux ever comes popular in Desktops it will end exactly same place, or probably beyond as anyone doing the customization probably knowns enough to be more dangerous and nothing prevents those changes...
Just look at many Android phones and how something like Facebook can't even be permanently removed...
And yet, despite Microsoft making money from licensing Windows, selling Office subscriptions, and (presumably) their App Store, they feel it's worth opening a firehose of ads on the user. I don't think that having a solid revenue stream and flooding the user with ads are related in any way; it's just a question of the company's morals and where they see value for/from the user.
Just look at many Android phones and how something like Facebook can't even be permanently removed...