I love my flip flops!
I usually plan on wearing my tennis shoes, and almost always wear flip flops instead. Soarin does make you remove them...but has a place for them on the ride underneath you, with your hat, glasses, whatever. If I am am a ride I think I may lose them I take them off and hold them in my hand. Just use your best judgement. And yes, they will be stepped on more time than you will be able to count!