Balances aren't a goal in themselves : Cold War is a good exemple of that.
Eventually, it's quite simple : the universalists ambitions of Hapsburgs (as well territorial than religious) were fought by...well, basically everyone.
Neighbours, Pope, Ottomans, Protestants, Germans catholics but not that fond of imperial hegemony...At some point, Charles had to make priorities in lack of men, ressources and money to fight all of these (the last 1/3 of this reign was passed to make peace with one side to fight the other one, in a Eastasia/Eurasia/Oceania way).
It's one of the reason, as well than inner issues, that his empire was eventually splittered in two halves for more easy managment (It wasn't the first occurence of this, of course)
So, I really don't think that refraining to crush Protestantism because you're threatened elsewhere, and because you lack ressources to do so, make you tolerent in the strictest (or largest) meaning of the word.
I would like to know your opinion about if Reformation would have been more successful it could have lead to scrapping Habsburgs (with HRE with them?), letting them to die out in some lost castle in Austria or Spain.