Actualy it's even more complicated than that..

there are 4 modes i know of

mode 1 as above,
mode 2 as above,
mode 3 left handed mode 1
mode 4 left handed mode 2

i guess thecnicaly there may now be a mode 5 with the single stick/slider throttle becoming more popular.

basicaly it dosent mattter which one you fly but most people fly the same as there instructor, our club has 1 instructor that can fly mode 1 and 2, he will teach you whichever one you want.

as for the history of why there are diferant modes......
one story i heard was that mode 1 developed from the early 2 chanel rc gear when rudder/elevator was on 1 stick, when more chanels were added naturaly they went on a second stick (aileron/throttle), why the new chanels ended up on the right side i've no idea.

as for mode 2... i heard that developed because full size planes had aileron/elevator on the joy stick and some bright spark thought it was more "natural" for rc gear to be the same (as much as rc is like flying a real plane. NOT).

i've no idea if these stories are true but then again may be they are.