Was waiting for a Kaepernick sympathizer to come out and beat that drum.....without turning this into a political discussion or dialogue the answer is very simple. Any employer or big business corporation, whether it be the NFL, Walmart, Amazon, McDonald's, TV networks, etc. considers the effect on their business and bottom line when making decisions for their companies. If they think something is too controversial to "carry" or sell they will choose to avoid it at all costs so as to not cause a loss in business revenue or bad press/boycotts. It's about losing sales/money and market share.
So, Manziel might still (maybe) sell tickets or attract non-controversial (at least political/majorly negative public) attention while Kaepernick won't and just cause a distraction and offend a chunk of the paying public, who will avoid paying to see him or his team and/or negatively affect the team's market.
To put it succinctly.... Kaepernick has every right to kneel, protest as he sees fit and stand his ground on his beliefs....and his prospective PRIVATE employer has every right not to hire him if it goes against their business model or concerns of impact on their "product".