1) Winner-take-all certainly flips the votes of all who voted against, for instance, McCain into votes for McCain when he gets all of the delegates from a state. Those votes cast in opposition to McCain do not count a bit.
2) Winner-take-all certainly moves the decision of who will be the nominee to much earlier in the process than otherwise. That makes all votes cast in states with later primaries moot. And the only way it is able to do this is... well, see #1 above.
I'm not saying it's bad or good. I'm just saying that's the way it is, and it really does ignore the popular vote.