I think this is just a selection bias — you're seeing it more than it is really there. I've heard more people say "Lyndon Johnson" than "John Kennedy" (nobody I know ever refers to John F. Kennedy as John Kennedy). Google Ngrams, which tracks frequency of word use across the Google Books corpus, seems to agree with me: for much of the late 20th century, the B and non-B versions of his name were neck and neck, though in the last 20 years the use of the B has declined.

One could more properly ask why JFK and LBJ more than other presidents are frequently known by their initialisms. That I don't know, but that seems pretty easy to establish. I suspect one would find the answer in looking at their campaign slogans (similar to Eisenhower referred to as "Ike"), but I don't know that for sure!