Well I don't believe Patriotism makes people irrational. I do believe there are irrational people who may take Patriotism too far. But Patriotism, imo, is a perfectly rational concept. Much like the devotion to one's own family, only on a much grander scale. Pissing on the flag....that's irrational.
As for the freedom others have died for, they certainly didn't do it with the sole purpose making sure everyone could piss on the flag any more than they did it to make sure neo-nazi scum could spew the craploads of garbage they do. It's just an unfortunate secondary outcome that haters exploit.