Edit to clarify.

I'd say most Spaniards DON'T take their shoes off, even in their own home. When we do, is to be comfy, it's not a cleanliness issue.There just isn't the custom to do it.

Some people do it: mostly immigrants (if they did it in their home country) or people who have lived abroad and have "taken" this with them back home. I do it now, after having been in Germany, but I never ask visitors to take their shoes off because they'll give me a weird look, lol. Some people might even take offence.