it sounds like you're making excuses for flaws in the movie so that you aren't dissapointed with it.

the only people that actually knew that they were in the matrix, were the ones that were told by people not in the matrix... some people had a feeling that something was wrong or whatnot, like morpheus explained to neo, but they never knew it... now that the machines will free people that want to be, i'm sure morpheus and everyone else will tell as many people as they can that they are in the matrix and they should get out and join the real world... and since the machines need the people from the matrix to survive, it all won't work out.