Berlin was off the table because Lufthansa, essentially the German airline for the entire Cold War, was banned from flying into Berlin (along with just about every other airline). And considering also that Lufthansa was initially intended for domestic service, it wanted a hub somewhere in the center of the country's air network. That ruled out Munich (in southeast) and Hamburg (in the north).

This left Germany with three airports: Duesseldorf (Rhein-Ruhr), Cologne (Cologne-Bonn), and Frankfurt. As for why Frankfurt trumped the other two? There doesn't seem to have been much of a reason. Frankfurt was sort of a stopgap solution; it was the one closest to the center of the five original airports and that meant it made sense as a temporary hub. And since Germany remained divided for nearly another four decades after Frankfurt was selected as that temporary hub, it just sort of came down to inertia. Too much money had been spent building up Fraport and too many airlines were now used to Frankfurt being Germany's international hub to really change.