I find his point about morality to be extremely valid. If you're doing something because you're looking forward to some amazing reward that awaits you in heaven or because you're worried about going to hell, then you have no morality. If you're doing the right thing because it's the right thing, that is true morality.
I believe it was Lawrence Kohlberg who listed five stages of moral development. Obedience out of fear of punishment is the very bottom-most on his list. Self-interest is the next highest. So, in other words, according to Kohlberg (and you may or may not agree with him), obedience out of fear of a wrathful god or with the hope of receiving reward from god are at the very bottom of a person's moral development. Certainly, not all religious people are at this stage. I don't think Penn's trying to assert that. But, it is true that most religions do teach that kind of morality.
At the very top of Kohlberg's list is the kind of morality that Penn is describing--that is using abstract reasoning to decide universally (not unequivocal--there may be exceptions) what is right and what is wrong and then to act accordingly. Such morality cannot result from dogmatic organizations. It cannot be the result of blind faith. It can only be the result of rational thought based on reality.
I also like that he points out that atheists really don't all agree on everything. We agree in one aspect--we all lack a belief in any god. But, aside from that, we have all sorts of different opinions. Some of us are liberal, some are conservative. Some atheists may even oppose gay marriage. But the whole point of being irreligious--the whole point of fighting against theocracy--is to allow people to disagree. Let everyone have their opinion on everything and disagree on everything. That's what it means to be a free thinker. You don't accept other people's ideas just because they say so--that's dogma. You listen to other people, weigh the pros and cons, and come to your own conclusion.
In this video, he laughs at Mormons openly. But, if you watch his other videos and find out how he really feels, you'll see he's not really laughing at Mormons, he's just laughing at Mormonism. Seriously, Mormonism teaches some pretty crazy things. And he's just laughing at those beliefs. He's laughing at the magical underwear. He's laughing at the whole story of the golden plates and the 116 lost pages of manuscript. But, he's very tolerant of people. He thinks very highly of people. In fact, he even says he doesn't think Romney's crazy--just that the teachings of the church are crazy. Of course, he resolves that by concluding that Romney doesn't really believe all of the crazy teachings of Mormonism. And, to be honest, I think that most people who claim a religion really don't believe the crazier things that the religion teaches. But, anyway, the point is that he's a really nice guy and he does have a lot of respect for people. Don't be offended just because he keeps saying "Mormons" and then laughing immediately afterward.