Why has the Japanese government continued to defer to the emperor throughout history?

First of all, please note that it is by no means accurate
to say that the Japanese government has deferred to the emperor throughout history. 
There has actually been only a very short time in the modern era when the emperor had
very much power.  Outside of that, the emperor has generally been a
figurehead.

The Japanese emperor holds his position because
he is reputedly descended from the spirits through the first emperor, Jimmu.  Jimmu was
supposedly a descendant of both the sun goddess and the sea god.  This made him and,
therefore, his descendants, divine.  However, this divinity has not typically given the
emperor that much power.  For much of Japanese history, Japan was ruled by shoguns with
the emperor as a mere figurehead.  This sort of rule lasted from 1197 AD to 1867. 
Around 1900, the emperor once again became a figurehead and power was truly held by the
government which was dominated by the military.  Today, the emperor has no real
power.

The emperor has status because he is allegedly
descended from the gods.  But this has not meant that he has really had power for much
of Japanese history.