B.-
My husband's granddaughter was visiting for Thanksgiving. She is 3 and is the same way. Everything was "why." It started to drive my daughter crazy (she's 12). But I explained to her that she was the same way when she was 3. That is how they learn. The brain of a 3-year-old is starting to think more complex thoughts.
When my daughter went through this, I tried very hard to not say "Because I said so," as I always hated this answer. When you get frustrated, just remember that the questions are your son's curiosity and his brain expanding. Sometimes I would turn the question around (especially if I knew she knew the answer...why do you think you should get down off the counter?).
Just keep it up. This too is just a phase.
Good luck!
-J.