Why is the HD the main bike of choice for a majority of MCs?
First, you have to know a little history of the HD company.  (see the links below).
Soldiers returning from WWII that used the HDs that the military bought, were now back in the US and wanting that same motorcycle they were used to using.  When these soldiers got together and formed MCs, it was the HD that they preferred.  Indian was basically the only other choice at that time. 
Honda's didn't really start showing up in the US market until the early 60s.  Hondas were not well thought of in the MC community, especially by many of those vetrans that had fought the Japanese.
One of the big advantages the HD had was that it was built in the US using the available US parts.  Many of these same parts were also used in the vehicles and farm equipment. 
To put it simply, they started the clubs using HD and it became the traditional bike to have.  In recent years, there has been many MCs that have relaxed those traditions to include other brands, including foriegn bikes.