Self-deprecation is something that I think you have to learn over a long period, and ultimately it seems to be about acknowledging your own flaws while embracing them as a part of who you are. Not to say that you shouldn't try to correct what you can, but the first step is to know that they're there. Comedy in general seems to turn around people being flawed and the world being an imperfect place where some stuff just doesn't make logical sense, and when you turn that inward you can really find out a lot about who you are. I tend to be distrustful of people who can't laugh at themselves because it indicates a blindness as to what's on the inside, an unwillingness to look critically at who you are and what you stand for. Perhaps not coincidentally a lot of these people tend to be extremely ideological and hard to deal with, so I really think there's something to that notion.
Basically, by embracing comedy you embrace the world as it is, full of all its imperfections and illogical holes, but at the same time not letting it get you down and depress you. Of course I'm talking about the good-natured comedy rather than the type intended to wound and hurt (looking at you, Family Guy and South Park, and I've talked about my issues with them at length) I mean the kind that makes you stop and think "What the fuck are we doing?" and then laugh at how ridiculous it is. I think that's one reason why Jon Stewart is the most trusted newscaster in the country even though he's a comedian, because he takes everything with a grain of salt he can cut through to what's really going on in a way that many people in the news seem to have lost.
So I guess the point of this is: Laugh at yourself, laugh at what you find ridiculous, and think. It'll make a better world.