Luckily, I've never had any problems with anybody, but I've only taped to the seats twice. Both times I asked the people if they'd mind and gave them my email address to email me for a copy of the show. That seems to make them happy. If you are really worried about it and there's a sound board area in the center of the venue, make nice with the board tech as they'll typically let you set up near their enclosure. Tell them you saw the band before and sat by the board and the sound was incredible...flattery always helps. That's where they are during the soundcheck and to see you noticed that the sound is better in that area is good way to ensure they'll let you set up near the board. Also be polite and say you have really close seats and are worried about bothering people with your stand, the fact that you are "going out of your way" to be sure not to interfere with the audience enjoying the show will earn you bonus points. An added bonus of doing this is there's usually security by the board, make small talk with them so they recognize who you are and you can rest assured that nobody will be messing with your gear because they'll know it's yours.
