The clock was designed in the 1940s by engineer and designer Hans Hilfiker (1901-93). According to Wikipedia, the clock has become a national icon.
However, Apple did not seek permission before it used the clock's image (shown above, iOS 6 clock and SBB clock, left to right). SBB said, upon noting the similarities (in a less kind manner, the fact that the iOS 6 clock was identical to its clock), that it was less interested in compensation than in bringing clarity to where and how Apple could use the logo.
In the agreement, Apple has given SBB 20 million Swiss francs ($21 million, 17 million euros) as compensation.
The clocks are still used in SBB's stations. You can watch a clock in action, in the embedded video.