How come no shogun ever tried to usurp the Imperial Japanese throne?

Essentially:

Tradition was a very powerful factor. The longer time the Imperial family doesn't get replaced, the harder it gets to replace them. The Japanese were already used to someone de facto being more powerful than the emperor in running government, first through the Fujiwara regents then the retired emperors. So it wasn't considered odd to have the emperor be more ceremonial or focus on the court/Kyōto.

No founding shōgun were in powerful enough position to do overcome that tradition.

On the founding of the Kamakura bakufu, it controlled only the eastern half of the country. Not to mention when Yoritomo revived the position of shōgun, it had fallen out of use for two and a half centuries. The position given by the emperor was Yoritomo's way of cementing his legitimacy, and in no way would it have been enough to challenge the imperial family's legitimacy.
When Ashikaga Takauji rebelled against Emperor Go-daigo in 1336, he got his ass kicked and had to run away to Kyūshū because his opponent had Go-daigo's imperial orders to vanquish him. He only recovered after he convinced Retired-emperor Kōgon to give him a set of imperial orders.
Tokugawa Ieyasu and his son Hidetada tried to marry Hidetada's daughter to Emperor Go-Mizunoo, hoping that from then on the Imperial line would be part Tokugawa (something many families tried to do before, with varying successes). A series of diplomatic faux pas in the 1620's by Hidetada caused Go-Mizunoo to abdicate the throne to his daughter (Hidetada's grand-daughter) without the bakufu's permission. This would dash Hidetada's dreams as a female emperor can't marry, so the throne would then pass to someone without Tokugawa blood after. The Hidetada went so far as to threaten to exile Go-Mizunoo, but in the end had to agree to the abdication. With the political stink from just trying to become a blood-relative of the emperor, imagine what would happen if he tried to replace the emperor.

The bakufu might have been later. They never tried so we'll never know. But for sure it would've been a lot more hassle than it was worth. For instance, the Purple-Robe Incident (who was allowed to appoint the ccountry's high-ranking monks) between 1627-1629 established that bakufu law trumped imperial order. So the only thing the bakufu would actually gain from replacing the emperor was control of a bunch of courtiers in largely ceremonial roles, and through the laws and bakufu agents in Kyōto they had great power over said courtiers already.