Flags are too vague for communication.

For many the national flag is a powerful and unambiguous symbol. Unfortunately, it represents a different set of ideas for just about everyone; its exact meaning is never clearly defined. Does it symbolize only the good aspects of a country, or only the negative, or all aspects? Does the flag represent the country as a whole or only its government? Is it a reference to the past, present, or future? Does it represent those who have fought for it? If so, they would have fought for a representation of themselves — a very circular activity.

When you involve the flag in speech you are using an extremely vague pronoun. Imagine using the word "it" with extreme passion. No one would know exactly what you mean, unless they happen to project as you do. What's clear is only that you are passionate, and clueless about your vagueness.
When patriots employ this symbol they are thinking of specifics, but aren't elaborating on specifics in the larger world context. When people burn the flag, they usually have very specific current events in mind, but the ritual is misinterpreted by the patriots as a disaproval of their own personal and perfectly noble ideals. And the patriotic use, on the other hand is misinterpreted by victims and critics of the flag's nation as approval of the clearly reprehensible. Hence the misunderstanding: "they hate our freedom".
Flags are just a terrrible way to communicate. They were invented for battling armies to identify themselves and to indicate the direction of the wind, so that weapons could be hurled with the proper force and angle. They serve to unify different interests against a conceived external entity.
Flags work well for aggression, but terribly for discourse.