This is how I see it.
Jerry's "I'll be the bad guy" comment is just him trying to get the players to buy into his directive and it's a bit of attention seeking on his part. Honestly, it's his team so he doesn't have to couch his decision, but since he's trying to appease both sides, sadly that was the best excuse he could come up with.
I'll also point out, there was absolutely no pressure at all on Cowboys players to protest until he opened his mouth. No one was looking at them negatively. There was no national pressure on Cowboys players to protest until Jerry opened his mouth. If he were the owner of the 49ers, got it, tons of players are kneeling and it's impacting your fan base. However, this story wasn't impacting the Cowboys much at all until Sunday night when he chose to open his mouth. Now he's pretty much painted his players into a corner, particularly minorities, where I'm quite sure their "blackness" (sellout, Uncle Tom, etc.) is now being called into question throughout their communities and via social media.
Simply put, Jerry pretty much threw lighter fluid onto the embers with his stand for the anthem mandate.