It's really not. This is the gesture for "siblings" (兄弟 or "kyoudai") in Japanese Sign Language.
Just like with spoken languages, sign language has evolved differently in different countries (here's a helpful list of sign languages). So, people who know American Sign Language obviously won't be able to communicate with people who use Japanese Sign Language.
In the West, the finger has long meant "Fuck you" for a very long time. In Japan, it traditionally has not. In American Sign Language, flipping the bird means, you guessed it, flipping the bird. In Japanese Sign Language, it does not.
So, Japan, what gives? Why the middle finger?
Japanese children are taught the names of all the fingers. The thumb is the "father finger", the index finger is the "mother finger", the middle finger is the "brother finger", the ring finger is the "sister finger", and the pinky is the "baby finger".
That's why in Japanese Sign Language, the middle finger would logically refer to "brother". There's a long cultural context.
In this video, you can hear the woman saying "ani" (兄), which means "older brother."
This dude too.
But here's where things get tricky! Because while traditionally, the middle finger isn't a profane gesture in Japan, many people in the country are aware of the bird, thanks to its appearance in Hollywood movies, foreign TV shows, and American musicians. There's even a Japanese Wiki page on it:
In Japanese, it's call the "fuck sign" (ファックサイン or fakku sain). In Japan, many might see it as more of a joke, and the Wiki does warn Japanese people about using it towards Americans and British people.
Yet, you do sometimes see it in Japanese media. This tough schoolgirl character flips the bird in the 2008 film Love Exposure. This certainly does not mean "brother." It means, "Fuck you." The image appeared on the movie's poster (though, it's unlikely that lewd Japanese hand gestures ever would).
And in case there is any doubt what is being referred to:
Oh! And similar gestures are used in Korean Sign Language and Chinese Sign Language.