Sounds like your channels are for the most part encrypted.
It works with WMC because Microsoft paid the big cost of licensing, etc and ensured that end-to-end encryption was in place (which is why you can only view live/recorded TV from WMC on approved Microsoft devices).
It makes sense because CableCARD requires much more than you paying your cable company for access.
Plex is extremely unlikely to ever choose or be able to make this work. See: Will there ever be DRM support?
