Disclaimers: I don't take offense from this kid's refusal to stand for the pledge. I agree with his position on gay rights. I absolutely agree with his right to refuse to stand for the pledge. The one thing I disagree with is whether this is a wise or appropriate way to protest. (but, again, you should have the right to)
For a lot of people. the pledge is now a symbol of this country like the flag is. For a lot of people, refusing to stand for the pledge is perceived as an act of disrespect for all the other things that the country represents, not just the things you're protesting. So it's kind of like flagburning (for a lot of people - not including me).
Now, I say the pledge even though I don't believe in God, and I don't literally think that the country provides "liberty and justice for all." Why?
Same reason that when I go to a wedding, I don't sit there silently while everyone says the Lord's Prayer. I may disagree with it, but I'll say it out of respect for the people there who do care about it. And they know my disagreement.
The pledge goes one step further because, as a symbol, it represents more than literally affirming allegiance to a country that literally provides "liberty and justice for all." I think of it as an affirmation that the country should provide liberty and justice for all and one's personal dedication toward those principles. And, personally, that affirmation is worth having to mouth the words "under God."