Your shower shoes pick up micro-organisms just like my feet do. But then you almost certainly put your shower shoes away wet, creating a perfect environment for fungi to incubate. You then proceed to carry them around in your gym bag, occupying the same space you use for clean clothes, toiletries, etc. Then tomorrow you'll shower wearing the same flip-flops that probably haven't even dried completely since yesterday, and you'll do so thinking that you're protecting yourself from grossness.
On the other hand, I shower barefoot, then dry my feet thoroughly and put on clean socks and dry shoes, thus creating an environment where anything I did pick up in the shower really won't be able to grow. Apply some clotrimazole cream once a week for good measure prophylactically, and I'm athlete's foot free.
I don't understand people who think they're being hygienic as they toss their wet shower flip-flops into the same bag as their toothbrush and deodorant.