Removing shoes when entering a shop or café used to be much more prevalent. Nowadays many don't seem to mind. They even stopped it at Samui Immigration in the last year or two, but many places still have signs asking that customers remove shoes, especially if they have polished wooden floors. I also find many pharmacies still request shoe removal.
I actually think it is a good thing, and we all do it at home. If the café owner gave her permission, then no problem, but it really isn't a big deal to kick off one's footwear. Perhaps she had a reason to not want to do it.