There's an oral tradition from R' Yaakov Kaminetsky that a tzedaka can have up to 49.9% of its costs as overhead, and still count as tzedaka vis-a-vis your tithing money.
Based on that, I've heard that some charity collectors do in fact take a commission (it sounds like that's just the reality, I don't know if anyone's ever asked about its propriety or disclosure requirements), and as long as the majority of the funds wind up in the right place, it's still considered charity.
Of course, you have every right to ask where your money is going, and if you'd rather contribute to something lower-overhead, that's your prerogative.
There's some evidence from the Cairo Geniza that in the times of the Rambam, a large chunk of the "holy fund" charity was going to "scholars and officials", and less than 50% was going to actual poor people. It's suggested that this influenced Rambam's view, which yells and screams at such a practice.