Q:

Why is "intrusive r" not stigmatized like other "mispronunciations"?

Why is it that dropping h's pronouncing (th) as (f), or using a flapped  intervolic t/d are taken as signs of poor education, when it's, objectively, just as orthographically wrong? 

A:

A pronunciation feature of a dialect is called a mispronunciation only when it is stigmatized.  When it applies to a regular feature of a dialect, like your two examples of r-insertion and flapping, that is simply what "mispronunciation" means -- saying things the wrong, i.e. stigmatized, way.
So if r-insertion and flapping are not stigmatized, they are not mispronunciations.  It is all a matter of terminology and social prejudice.
Your use of the phrase "orthographically wrong" suggests that you have a theory about "correct" pronunciation that all and only the letters used in the conventional spelling of an expression should be directly reflected in pronunciation.  That is an unusual idea, but if you have that prejudice, you do, and it's not the sort of thing that we can argue about.  I don't share it, though.

