- "I take it that your question has to do with what my perception is of being a good teacher, isn't it?"
- "I take it that your question has to do with my perception is of being a good teacher, hasn't it?"
In all honestly, the sentence is convoluted in both instances. If you're writing this a as piece of fiction, you might be better off rewriting the entire sentence. To answer your question, however, "hasn't it" is proper.
Go back to the root words and ask yourself if they make sense.
"Your question has (root: have) to do with . . . is it not?" The last part is basically similar to a resumptive verb in some languages, picking up the action of the primary verb of the sentence. Here, have means to possess, to hold, whether literally, or metaphorically. Is means to exist, to be. Since the definitions are no where similar, the second verb cannot be resumptive of the primary verb.
"Your question has . . . has it not." These are the same words, and therefore, the resumptive verb matches the primary verb. You are therefore right, this sentence is the proper one.
If you want to put emphasis on "I take it," move it around in the sentence. "So, I take it then, that your question has to do with my perception of what it takes to be a good teacher. Is that right?" Notice in this sentence, I've managed to separate "I take it" to give it emphasis. I also broke "Is that right" off into its own sentence. Now, it is no longer resumptive, but rather, is asking if the entire question, in the way that it now exists, is correct.
Hope that helps.