Some of the teams are immensely profitable, while they have all increased in sale value due to the League's success. It may be aggravating to have to turn stupid and thuggish but athletically talented ball players into often vainglorious and preening multimillionaires, but the burden is slight. Lush TV contracts, favorable tax treatment, public stadium subsidies, and owner carve-outs of ancillary profit streams make an NFL team a good way for rich owners to get richer while having a lot of fun.
The greatest risks to the NFL are: (1) that concern for chronic brain trauma degrades the traditionally bruising and crowd-pleasing character of the NFL game; and (2), that the decline of the network and cable TV financial model diminishes their ability to pay the NFL outsize fees. Those issues are far more worrisome than the Colin Kaepernick problem.
Actually, it would have the exact opposite effect. An effective salary cap would lower the cost to the owners. If ticket prices remained at their current rate, profits would soar. However, it would make more sense to lower ticket prices a little to expand that market. I took my son to a Colts game 10 years ago and with parking, a hotdog, nachos, and a soft drink for both of us, plus the cost of tickets was over $110. I haven't been back since.