Okay, this metaphor has been stretched to its breaking point.
Speaking literally, shepherds might be perfectly nice people, but they eat sheep. More than wolves do.
Sure, shepherds might seem to protect a sheep from a wolf, but a large wolf might seem to protect a sheep from a smaller, weaker wolf. The shepherd's just the biggest, most cunning wolf.
I think that's alternately funny and sad... It's funny because Christians like to accuse atheists of being wolves, and say that their shepherd will protect them from us nasty, nasty wolves, but really a sheep has far more to fear from its shepherd than it does a wolf.
To say, "I am a sheep, you are a wolf, my shepherd will protect me from you..." the sheep in the analogy subjects itself to a terrific threat to protect itself from a minor one. Out of fear of a small wolf it submits itself to a great one.
Sheep are destroyed in great numbers by their stupid reliance on a protector who does not have their best interest at heart. That someone would disagree with me, then immediately compare themselves to that dumb creature... I can't help but laugh.
It's sad because the truth is no one ever wrote a list of threats for disobedience, impossible rewards for obedience, and rules for avoiding everyone who isn't part of "the collective" because they've had anything but their own selfish interests at heart. It's the sort of thing said by the kinds of people who, at the very least, want to keep the option to spend human lives like currency open. They need their followers as dumb as sheep for it to work, though.
That's why it's so important to keep them separated from dissenting ideas, to teach them to value obedience over their own wisdom.
A sheep is a stupid creature that dooms itself, and for someone to haughtily compare themselves to it makes me laugh a little. But a sheep is also a tragic creature, and when the analogy holds true it's sad.