It depends upon the question, and how it is asked. One of my favorite students commonly asks questions about the effectiveness and/or reasons behind doing things. I love it, because I know I'll never put something in front of him without being able to explain why it is useful. I keep classes pretty informal, and have made it clear I have no problem with his questions. He is always respectful, and just wants to understand and make sure he knows the reasoning behind the art.You should be able to ask your instructor questions. You should be able to voice your concerns. There's a caveat however. This should be done at the right place and time.
Questions or concerns about how the class is run or why something's in the syllabus or not in the syllabus should be addressed outside of class and in a one on one setting. Asking "why are we spending 30 minutes on warmup" during warmup puts him/her on the spot. Asking "why are we learning this, it'll never work" during the drill won't and shouldn't go over well.
Asking during a one on one conversation should get you honest answers. They may not be the answers you want to hear, but they should be honest. Your teacher owes you that, because he/she is your teacher. IMO a teacher owes it to his/her students to teach/explain the why and why not.
A teacher doesn't owe the student a custom curriculum, unless that's part of the agreement. I joined my dojo because Seido karate is being taught there. My teacher doesn't owe it to me to teach me BJJ submissions, Escrima tactics, nor ninja star throwing and disappearing acts. He owes me the Seido syllabus in and a proper progression and in a reasonably safe environment, and the way he teaches it and nothing else.
If I appropriate ask why, I should get an appropriate answer. If I can't accept his appropriate answer, I should find another place.
I mention this because his first few questions would probably have gotten him stern looks from some instructors, because they seemed like a challenge to the effectiveness of the techniques. I gave him some leeway early, because I believed him to be earnest in his questions.