No, you go through bag check before you board the monorail at each monorail resort.
@networkpro is correct, once you get off the monorail, you are mingling with other guests who took the bus, drove their own car or got to Epcot via some other form of non-monorail transportation. I don't think there's any way, short of redesigning the entire entrance, to separate monorail passengers from other guests entering Epcot.
I can't remember. Is there bag check at the TTC before you get on either the express or Epcot monorails? I've only parked at the TTC once and I believe it was right before they implemented security at the resorts.