I'm not sure about why that's the standard, but it may have to do with the fact that in fighting games you don't want to be jumping all the time, it's something that you have to do carefully, while crouching is something you do constantly, and most motion inputs involve the "down" direction (like quarter circles or the shoryuken input), and having left-down-right lined up makes it pretty easy to do those motions. Think about pressing your Q-W-E keys in quick succesion. You can probably do that without much practice. That's a half-circle-forward motion. If you have "down" in your thumb, a half-circle would be like pressing "Q-Spacebar-E" in quick succesion, which is more difficult.

Maybe it's also because people often use the space bar in keyboards to jump in many games, and that's what they were used to.

In any case, once you get used to this layout, it's very comfortable.

The down button is used constantly and used with the directions to input quarter circle motions etc for special moves. It would be very awkward to have down under the thumb. Up should be used much more cautiously and purposefully.

Other layouts are possible and some people find the WASD layout more comfortable. Some even end up using keyboard buttons for the left hand in WASD layout with arcade buttons on the right (a.k.a. mixbox).

The person commenting above you seems surprised by this "all button" design, but this is becoming very popular for its precision compared to stick or controller. And it's no different using WASD keys to walk around in an FPS game rather than using an analog stick on a controller. If you play fighting games I'd highly recommend trying a leverless controller like this.