After the war, the division of Germany - and Berlin itself - was expected to be a temporary arrangement, and the West German government were wary of choosing one of the bigger cities as capital - Hamburg, Cologne, Frankfurt or Munich, for instance, in case it looked like they were accepting the status quo.
So Bonn got the job, largely through the lobbying of West Germany's first chancellor Konrad Adenauer, who just so happened to have a house in commuting distance. The vote which decided against Frankfurt (which had been the site of the first German constitutional convention during the Revolutions of 1848) was Decided by One Vote. The public dryly referred to it as the Bundeshauptdorf (Federal Capital Village).
The West German government had to put up with a motley collection of temporary and converted buildings for decades, because building new purpose-built governmental headquarters might likewise signal the final acceptance of a divided nation.
The West German government finally gave up and commissioned a "proper" governmental quarter complete with a "Museum Mile" - in the late 1980s, just before the wall fell. Even governments weren't immune to The Great Politics Mess-Up.
Since the reunification, it's managed to retain about half of the government jobs (too expensive to move in many cases). Much of the "new" governmental quarter has still never been used. Due to its history as German capital the city is allowed to call itself Bundesstadt (Federal City) although it has always been a part of the state of North Rhine-Westphalia rather than a city-state like Berlin or Hamburg or a New World-style federal district like Washington, D.C., Canberra or Brasilia.