Look, I'm no conspiracy theorist. I truly don't see the benefit of 'Sports Illustrated' holding some company wide meeting in the conference center to discuss subliminal ways in which they could recognize the increasingly polarizing National Anthem hoopla. Hell, I don't even feel right in making the assumption that the people with final edit on these covers decided to let their personal belief in and/or support of Colin Kaepernick's cause seep into their work.
The being said, IF they were to decide to lend a subtle "nod" to the public protests that some would consider a plague on their oh-so-important separation of sports and "politics", this is literally EXACTLY what it would look like. I mean, four All-World football players being in a position that's as foreign to them as kneeling? Two of those players - who are being highlighted for their unbelievable offensive efficiency - potentially being down by contact in their photos? The odds of that happening incidentally are probably just as low as the odds of having the most recent critic of the person that popularized said pose (LeSean McCoy) be the one peer who was picked to get awkwardly and unforgivingly photoshopped onto the taints of those performing it.
But no, I won't say that this was the result of someone cleverly getting their point across in a way that could be easily explained away if they were questioned on it. After all, I wouldn't want to "read (a lot) too much into" the fact that four NFL superstars were pictured in the exact same position despite that position being such a rarity for people that aren't using it to publicly push for equality.