I believe when a 'bottle' is made out of paper, it's properly called a 'carton'. e.g. a 'carton of milk'
The mystique of ultra high-end wines aging for years requires careful conditions, specific wine properties, and is still pretty hit-and miss. For everything else, there's no reason not to package it for convenience rather than tradition.
Boxes used to be used only for bad wines, and there's still plenty of bad wine in boxes, but they've gotten good at making decent reliable wines for cheap. Putting them in a box lowers costs, and it's very nice to be able to take out one glass at a time.