I am not a defender of the NFL (did not watch a single game yet this year) but how can you accuse the NFL of encouraging flag disrespect? AFAIK no one in the NFL, including the players, has encouraged disrespect of the flag. The players who kneeled did so in protest (of something or other) while the anthem was playing. The flag was not burned, stomped upon or otherwise disrespected.
As far as your second point, the protests have been met with a variety of counter-protests and that's OK. Just bear in mind what you are protesting.
And, as far as ticket prices.....the teams will charge whatever their fans will pay. Nothing more American than that.
Personally, I see a much greater negative impact to football fans by the constant and intense second guessing of plays by announcers, "experts" and officials. As I write this the winning TD is being questioned unnecessarily although the correct ruling was made.