"than" is usually unstressed, which means it's going to be largely reduced to a schwa. "then" would also be reduced to a schwa if it were unstressed, but it doesn't seem to be as frequently unstressed. When trying to transcribe the spoken thought to written text, the unstressed schwa is a lot closer to the 'e' in then than the 'a' in than, which probably explains the predilection for choosing "then" when "than" is meant.
(I know I have a major tendency to write "then" when "than" is meant).
I would never have said they were homonyms. That said, they're probably closer for people speaking with a bit of a Southern drawl than they would be with standard American pronunciation.
(I know I have a major tendency to write "then" when "than" is meant).