I've been doing it since 2011. and I wrote up a how to do it guide here:
1) gives you as close an approximation as you can get on a TLR of which situations are likely to induce flare
2) give protection to the viewing lens
3) Due to #2, I no longer need the lens cap. I just keep the hoods on all the time
4) If you put a hood only on the taking lens, the camera tends to flop over inside a camera bag.
5) Because you can.