It won't work
It won't work, because too many sites are built around the assumption that they can set cookies, run Javascript, and so on, and break without it.
So, you either have to:
1) Make the protection really prevent tracking but ship with all the protection off - most people will not activate it, most web sites will break if you do activate it, and it won't be any different than running NoScript and CookieMonster.
2) Ship with it enabled but make it just an advisory flag, and trust the web masters to honor it - you will be tracked, just as you are now, because there is too much money in tracking (or so the perception is).
3) Ship with it enabled, make it prevent tracking, and break most web sites - again, like NoScript and CookieMonster, but with lots of angry users and angry web masters. Won't happen.
The *right* answer is to make browsers NOT accept cookies by default, NOT run Javascript by default, NOT run plugins by default, and instead prompt the user when a site wants to do these things, and let the user decide Yes/No/Just this once, and MAKE the damn webmasters aggregate their fecal matter and stop making their sites NOT work if you refuse.