Bypass temporarily disables a plug-in without losing any settings you've made in it.
It's not just related to Automation, you can Bypass any plug-in down in the Smart Controls panel by clicking on the little power symbol in the left side of the plug-in slot. With Automation, you can have an effect set up and Bypassed, and then Automate it so the effect happens only at certain parts of the song (like, maybe, an echo effect that only kicks in during the choruses)..