As a professional IT engineer and general power user (Linux, Windows, Android, OS X, iOS) as comfortable in command line interfaces as graphical, I use the tools at my disposal to achieve my ends. I could not imagine using an Android device that isn't rooted, and I'm normally loaded with a plethora of utilities that require it. At the very least, I enjoy the freedom of controlling the obligatory bloatware that normally comes with my favourite device, inserting my own system apps, and making legitimate modifications for aesthetics, comfort, and convenience.
I have been forced down some dodgy avenues just to achieve proper functionality in apps whose authors choose to cripple rooted users. Being told that my device has 'unauthorised modifications' by (for instance) Virgin TV Anywhere makes my blood boil, and I'll happily break their code and contravene some license agreements if it's the only option available to me in pursuit of expected functionality.
In this regard, I agree that you're inviting a lot of users, whether through indignant spite or mere utility, to foil your efforts should you choose such a draconian path as the aforementioned media application. This might even encourage piracy of your app altogether when 'fixed' versions of your code become more prevalent as torrents than your legitimate sales.
Personally, I always go for the paid option, even when I'm forced to swallow my sense of security and break it with tools I scarcely trust in order to make it work. For many, though, the initial exposure they'll have to your product is through nefarious channels, and they're hardly going to go paying for the legitimate and hopelessly crippled version.
I understand why some coders are forced to make these choices, and its good to see sensible questions asked about the right way to protect intellectual property.
It is even more reassuring to see sense in the answers.
Just my tuppence.