By default, Ponyhoof will run for all Facebook accounts on the same browser and computer.
There are two Multi-user options at Ponyhoof Options > Misc. If you want to only run Ponyhoof for yourself, you can untick both of those options to make it exclusive to you.
Note that Ponyhoof Options is still accessible by disabled users.
The best way for this situation is to use your own Google Chrome Portable or Firefox Portable. Both of these portable versions let you put your favorite pony stuff without sharing them with others!