When I look throughout Japanese history, nearly everyone serves or is under the emperor. Even under Daimyos or Shoguns, they all seem to fight each other but not against the emperor himself.
The Japanese have had an emperor for nearly or literally all of their entire history.
Has, let's say, Japanese Christians revolted? Shintoism seems to have the emperor as a divine figure, but Christianity thinks otherwise.
The emperor bloodline has existed for centuries, did anyone in Japan think "Hey why is this dude ruling!?" Or "This guy isn't that great!" and started a revolution?
I know Shoguns were thrown around, but what about Emperors?
There are two different ways to take this question:
Did Japan ever had anyone revolt against the imperial institution, with the aim of replacing it with another form of government or with their own family?
No. At least not that I know of after the establishment of the Yamato dynasty. If there were it's lost to history.
Did Japan ever had anyone revolt against the person of the emperor or the political faction led by the emperor?
Yes. Three incidents come to mind off the top of my head:
Hōgen War (1156) - At this time the de-facto head of state was not the emperor, but the retired emperor, and had been this way for quite some time. However on the death of retired emperor Toba, the court broke into two factions. When Toba first retired, the throne was passed to his eldest son the emperor Sutoku. But Toba forced him to abdicate for his younger brother emperor Konoe. Sutoku remained powerless, as Toba was alive, and when Konoe died prematurely, Toba passed the throne to another son, the emperor Goshirakawa. Then Toba died himself. The imperial regent Fujiwara family had also broken into internal dispute as well between a Fujiwara who held the official position of regent and a Fujiwara who was head of the clan. The court was split into those who supported emperor Goshirakawa and the Fujiwara regent and those who supported retired-emperor Sutoku and the Fujiwara head of clan, and war broke out. Goshirakawa's side won.
Jōkyū War (1221) - the Kamakura Bakufu originally had a good relationship with the court, but that relationship deteriorated after retired emperor Goshirakawa's (the same one) and the founding Shōgun Minamoto no Yoritomo's death. In 1221, the retired emperor Gotoba issued orders to fight against the Bakufu's de-facto head, the bakufu regent Hōjō Yoshitoki. The result was a stunning failure. Retired emperor Gotoba was exiled, his supporters were exiled and their lands confiscated, emperor Chūkyō (who was not yet three years old by modern count) was forced to abdicate.
Nanboku-chō period (1336 to 1392) - Emperor Godaigo began "rebelling" against the Kamakura Bakufu in 1331. Though he was captured and exiled, he came back, and his supporters was able to overthrow the Kamakura Bakufu in 1333. In the aftermath, lingering resentment from the Bakufu's supporters, internal factional conflict, and bureaucratic confusion chipped away at support for Godaigo's goverment. Fearing revolt, Godaigo issued orders in 1336 against one of his important supporters in 1333, Ashikaga Takauji. Takauji decided to found a new bakufu, the Muromachi Bakufu, and to support a different imperial line to be emperor, and raised up to the throne the emperor Kōmyō. The resulting wars went back and forth and continued long after the death of all the instigators until 1392, when Godaigo's descendants on the verge of defeat agreed to peace terms and accept the Gokomatsu empeor. The Bakufu ended up not upholding those terms.
EDIT: I feel I should mention one more case. Taira Masakado after he forcefully took control of the Kantō, declared himself the "New Emperor" in early 940. In the letter he sent to regent Fujiwara no Tadahira, he said that as a fifth generation grandson of the Kashiwabara Emperor (Emperor Kanmu) it should not be out of his destiny to control half the realm. He refered to Emperor Suzaku as "Original Emperor". So it seems he didn't want to overthrow the emperor. Whether he wanted complete independence in the Kantō or just a separate government (under Emperor Suzaku, but not controlled by the court) is up for debate. Whether that counts in your definition is up to you. His rebellion was crushed in two months.