Ahahahahahaha no.
The difference, my friend, is the virtue of our two kneeling groups.
Despite the subject matter, I'm NOT talking about the "do good deeds" nice-person-at-church virtue. In rhetoric, a virtuos person meets the expectations of the audience. (Meeting audience expectations is called 'decorum' in rhetoric).
Donald Trump, for example, has impeccable virtue with his base.
People in Church kneel because kneeling before God is the norm. However, we don't usually kneel before the flag as a sign of respect. Doing so in fact violates the decorum of a huge swathe of the American audience. People of virtue are expected to stand for it because the flag itself stands for the perfect ideal of liberty and justice for all.
The soccer players, in kneeling for the flag rather than standing, are not therefore being virtuous because they evidently have an issue with those ideals.