|I took training at work a few years ago that involved standing up in front of the class and presenting some material while being questioned and sort of hassled in an attempt to prepare the student to operate in that sort of environment professionally. Needless to say, I hated it, I've never encountered anything even remotely close to that in my professional life, and if I did, I'd quit on the spot. Anyway.
One of the things the teacher criticized me for was for saying, "That's a good question," when he asked questions during my presentation. His logic was that high-ranking people don't need to be complimented on the quality of their question. Whatever, bro.
I realized I say "that's a good question" a lot when I'm presenting something, typically in a work setting. My primary goal is to communicate, and that involves both the sender and the receiver. I'm typically not standing up and speaking in front of a group of people for fun, so if my audience doesn't understand what I'm saying, that's a failure. Since I usually don't know the background or experience level of each person in the audience, I do a mix of dumbing it down and avoiding jargon. If somebody asks me a question, it usually helps me clarify something, or add more detail to something I might've glossed over, or even include something that I neglected to mention earlier. In any of these cases, my audience is gaining a better understanding of what I'm saying, which is the whole point. When I say it's a good question, I mean it.
So if you're the kind of person who thinks "that's a good question" is somehow patronizing or offensive, you can feel free to shove it directly in your ass.