To me there’s a big difference between “elitist” and “elite”. Honors programs are by definition elite; the students have demonstrated superior academic performance and (in many cases) are willing to tackle a more challenging curriculum in college. That is elite.
“Elitist” is when the students in that program believe they are entitled (to special treatment, perks, whatever), unwilling to fraternize with the great unwashed masses in the "normal’ program, and feel generally superior. It seems clear that the programs can be elite without being elitist, and I would hope most programs attempt to foster that kind of environment.