Java allowed Minecraft to run pretty much everywhere, including as an applet (very important in its early time) and it relied (and still relies) on LWJGL which provides access to the most common stuff you'd need to make a game (OpenGL, windowing, input events, etc) - and at the time it also worked for applets too (you needed to download the LWJGL applet code but it was signed by the devs so you didn't get too many scary messages).
I used the same tech (Java+LWJGL) at the time to make a few simple demos/games and it was quite easy to make stuff - e.g. i made this[0] in a few hours using Java, LWJGL and Eclipse on the iMac i had at the time.
He used LWJGL, which probably covered a lot of his library needs.
Java has a JIT, so it's not comparable to Ruby and Perl.
It did not start being popular :)
Seriously though, I think Java helped it get so much traction initially. Writing mods was tedious but not that difficult, and it was multi-platform for free. Nowadays I assume the vast majority are playing bedrock on consoles or PC, but at the beginning it was rather nerdy and being playable on Linux and Mac was nice for some tech-minded people.
Given what it was in the very beginning versus what it very rapidly grew into, I guess it was just something that made sense at the time.