While Charles is no arbiter of what is good, right or holy, I sympathize with his choice against TEC. Owing to the historic anti-Catholicim of the royals and the British public in general (many have no clue how they feel about Jesus, but they know they hate the pope), his attendance at a Catholic church was sadly out of the question.
Well, he does turn up at Orthodox churches from time to time (and is a major donor to the Mount Athos Foundation). I guess he was giving a nod to Scotland by going Presbyterian on his last visit here.
I think the rationale for Charles avoiding any Anglican type church was to not create a scandal and to not insert the Windsors into the problems of the Diocese of Pennsylvania. At least Charles went to church.