Honestly, why does it even matter? You can talk about Judaism no matter what forum heading it is under. So why all the commotion?
Do you think we're trying to slight Judaism or something by placing it here? It's just here for organizational purposes, not to try to insult its followers.
If, as you suggest, we tried to classify religions based on where they are PRACTICED... well, we'd have a problem. Today Judaisim is practiced in the "East" and the "West"... as is Christianity, Islam, Buddhism, Taoism, and many other religions. It would therefore be pointless to try to put them under a present day location heading, because instead of "Western, Eastern, and Alternate" headings we could only have one heading titled "Eastern and Western Religions". And we can't list them according to populations, because then we would have Islam, Christianity, and Judaism in one folder with ALL their topics (impossible to navigate) and the rest of the religions in one or two other folders (which makes it look like we're giving preference to the main world religions rather than treating everyone equally.) Finally, we can't list them ALL individually under the main page without headings, because then the main page would be too long and difficult to navigate.
So, that leaves us what?