Standing is not respecting the flag. Plenty of people stand for the flag who despise the things the flag stands for, like freedom of speech, expression, to have a different opinion. They care more about the symbol than they do about the nation.
Kneeling is not disrespecting the flag. When the whole thing started, Kapernick (who i think is a bad player and a self-righteous rear) went to a series of veterans and asked them what he could do to make a statement while still respecting the flag. They suggested he kneel.
If you equate standing with respecting the flag, you are making a political statement. To the people who consistently whine about that, they are saying the only form of patriotic demonstration that counts is the one they themselves support. i can't think of anything less American than that.