Thongs in the rain solve a very specific problem: water invading your boots and taking up residence there. Once your stuff gets wet, it does not dry out, at least not on any prompt timeline. I've spent many futile afternoons with my shoes waterlogged and my otherwise protected feet soaking in a dumb swamp prison. You might have also inadvertently owned yourself in the same way.
The middle ground of wet weather footwear is no place to live. You can either go all-out and encase your feet in tank-like apparatuses to protect them from every drop of water or you can embrace freedom. Allow me to make the case for the latter option.
Your feet will get wet if you wear thongs in the rain, obviously, but the hidden benefit of open-toed rain shoes is how quickly they dry. Imagine, if you will, arriving at your destination with wet feet but being able to walk about just five minutes later as if had never been raining on them all. Sure, your feet could have been dry the entire time, but that means you'd be carrying an extra few kilos worth of soles and complicated waterproof leathers. Also, that's the coward's way.
Obviously, this won't work for everyone. Additionally, if you work in a lab or a wood shop or some other place of work that requires close-toed shoes, ignore away. Perhaps you only own crappy shower-shoe thongs unfit for the slings and arrows of the outside world. It's fine! Accept the wet embrace of marshy footwear.
But if you want something better, if you are unafraid of walking through a bit of water for unencumbered, dry feet, try it. If you don't like it, you can always go back to swampy living.