It's polite to say "you can" if you're letting someone know it's okay by you to do something that may be more convenient for them. You should only use it if you're fine with them choosing not to do that thing. It's rude to say "you can" when you're asking someone to do something for you.
This means it's fine in your example. The driver can drop you at the gate if he likes, or he can drive you to your front door if he prefers. I've personally said something similar to lots of drivers. They sometimes say okay and stop, and sometimes they insist on driving me all the way. I'm fine with them choosing either option, as you seem to be. Telling them about their options is perfectly polite, but you should make it clear that you're okay with them choosing to drive you all the way instead. "You can drop me at the gate instead of driving the whole way, if you prefer" is better than "you can drop me here, please", because the latter sounds like you're requesting for them to drop you there rather than giving them an option.
A counter example is if you asked the taxi driver to drive you home and then changed your mind halfway there and decided you'd rather go to your friend's house. If in that case you said "actually, you can drop me at my friend's house instead at [address]", that would be very rude. The difference is you are asking them to do something for you, which they may or may not actually want to do. To be clear, it's absolutely fine to ask a taxi driver to change their destination, but you need to form it as a request which they have the agency to accept or decline, rather than tell them they "can" do it.
Another example that's in a restaurant setting, since that was your original question. Say you are seated at a table with more chairs than intended, and for some reason you don't want the chairs there. Telling them "you can take these extra chairs away" would be incredibly rude, because you have no reason to think they have any desire to do that. However, if you saw them trying to scrounge up chairs for a large party, it would be very kind for you to call them over and say "you can take these extra chairs". Again, the difference is whether you are requesting something you want versus letting them know you're okay with them doing something that will be helpful to them.
A simple test is to ask yourself, "if they chose not to do this thing, would I be upset?" If the answer is "yes", then you are making a request, and you should phrase it with "can you" or something similar instead. If the answer is "no, I'm fine with it either way, it's completely their choice", then it's okay to say "you can", although you should make sure it's clear that's the case.
