Well to be fair, Kap did make it about the flag (but not the veterans) with this quote here: "I am not going to stand up to show pride in a flag for a country that oppresses black people and people of color." Do I disagree with them kneeling? To an extent, yes but I don't believe it's disrespectful to the flag or the veterans.
Speaking of which, the flag itself is not being disrespected. Now if folks say that it's disrespectful to what the flag stands for (no pun intended), then I'm all ears. As a matter of fact, when the kneeling first started, I specifically remembered that there was a trend on Twitter called #VeteransforKaepernick (still around if you search it) where a number of veterans supported Kap.