I have a couple schools of thought on this one.

1.) If you need to make an emergency landing, or are in an emergency on the place, your feet are going to get trembled. Ideally you should wear some sort of shoes that you can run or swim in (worse case scenario)
2.) if you do wear flip-flops on a long flight, be sure to bring warm socks. Sometimes they turn up the AC and then you are screwed!
3.) A he benefit would be going through security, and being able to just kick them off to get more comfortable on a flight.

SO, it's sort of up to you. Depending on how much carry on baggage you are taking, and option could be to wear flip flops until you are on the flight. then keep a pair of shoes in a carry on bag under your chair in case of an emergency, and also a paid of warm socks to be comfortable of your feet get cold.

Phew!!! A lot to think about!