Like so many common mistakes, most people DO actually know, but can't be bothered to pause for a second to get it right. If you offered most people $100 to write sentences using 'than' and 'then' (and there, their and they're too) correctly, I'm betting almost all would get them right.
For the specific issue of people using 'then' when they mean 'than', I've believed for a long time now that it's caused by the brain focusing on the comparative ending, which usually has an 'e' in it. For example: Bob is taller than Sue. As you write 'taller', your brain is focused on the final 'er', and automatically makes you type 'then' instead of 'than'.