Silly rationalization, sort of like asking if God can nuke a burrito so hot even He cannot eat it.
Part of being free is being free enough to criticize what's made you free. Because if you're not free enough to that then freedom isn't worth much. The Flag isn't necessarily just a symbol for freedom it's a symbol for America and what America does and stands for. And if you feel what America is currently standing for isn't right then burning a flag symbolizes that. That America is doing something that's in opposition of what it stands for. (This, of course, applies to any "domestic" instances of flag-burning. Foreign flag burning is more about hate.)
Burning a flag isn't saying you "hate freedom" its saying that you hate what America is doing in the "name of freedom." Flag burning during wars, for example. Makes sense when you oppose the war because you see your country doing something you think goes against its values and principles so the flag as a symbol is meaningless since the principles it stands for are, apparently according to the war, not important.
Burning the flag isn't about hating freedom or doing "because" of freedom. It's strong symbol that you think what America is doing is wrong. So next time you see a man burning a flag rather than yelling at him, saying he hates America or trying to stop his freedom of doing so; why not ask him what he thinks America is doing wrong to make the flag's symbol null.
Many Americans want to react from the gut and emotions without thinking and discussing. So we see someone burning a flag, a group of people wanting to build a community center, or things like that and we get angry and think it's against America. Rather than, you know, discussing things and finding out what the real story is.
Don't get angry at the man burning a flag or protesting an Army recruitment center or things like that. Instead, try and find out why he's doing it. You might learn something.