T.C.
Hi S.,
I'm an OT who works in a local school district. I agree with the other Moms who say this sounds like a sensory processing thing. I've met and worked with a number of kids who don't like socks and shoes, and the feel drives them batty. One boy in particular did okay if his shoes and socks were a size too big. This meant they didn't always stay on just right, and he got a lot of sand in them (which made ME cringe, but not him, lol).
Something to consider is some sensory re-learning. Take him to the store and have him choose a pair of socks he thinks feel "okay" on his hands. Every day, have him rub or touch the socks on his own feet (you can even start off with the flip-flops still on his feet.)
Over time, he should be able to eventually pull them on and leave them, and even rub his feet while he's wearing them. Then he can work up to walking around in them. Do the same for shoes.
A small caution, try to avoid making a big deal out of it. Any child learns quickly how to manipulate what they want out of Mom and Dad, and sensory-integration quirks are not an excuse. If it's his "job" every day to put socks on and "get used to them," will help him to get over it faster than, "Johnny just doesn't like shoes and socks." (making excuses vs. teaching him how to cope with it himself)
He's got to deal with it eventually anyway (school uniforms, ski trips, college, career, etc), might as well learn how to cope properly while he's young, right?)
Hope this helps :)
T