While that is true, that doesn’t make the languages anything other than English and French, and using the flags for depicting them is established and well-understood worldwide, even in countries which have a bad association with 
or 
.
What would you use instead (worldwide, think tourist signs and such)? I think ISO codes will not work well as icons for this any time soon … List of ISO 639 language codes - Wikipedia
I could rather think of an argument about languages not associated to a country with a flag, but that should have come up somewhere already, I guess … 📊 Language Tags - "Final" Vote