Both pokemon actually get flare blitz as their best physical fire move - flareon learns it at lv. 45 and rapidash at lv. 49, so not too huge of a difference (unless you plan on using flare blitz against kiki or something ) And if you want to avoid recoil, the second best physical fire move would be fire fang for flareon, which outranks rapidash's flame wheel by a lil' bit.
Rapidash is probably the more well-rounded of the two (and is probably the superior choice if you're just pitting them against each other), but neither of them are gonna be taking many hits anyway (especially with flare blitz's recoil), so personally I don't feel like it means much. i think it really comes down to your playing style and which you think you'll have more fun using ^^; or you could decide purely on aesthetics, since they're similar enough in terms of use anyway
Overall I'd say, if you've ever used one of them before, go with the one that's new to you or seems like more fun.