People take a knee to propose, to be knighted, and in general to honor the person or object they are kneeling before. Kneeling before the flag is absolutely respectful. Because it’s not the “traditional” posture, it’s also a protest, but one that’s done respectfully.
Sitting, ignoring the flag and anthem — that would be disrespectful. So would standing with one’s back to the flag. But kneeling? There’s no instance I can think of where it’s a sign of anything but respect and honor.