Doing the "both sides" thing is kinda lame, here. First, noting that somebody is irresponsibly censoring certain things isn't about being offended. It could be about calling attention to the way somebody is irresponsibly censoring things, because it's irresponsible. Second, even if this were just about people being "offended" (and I think what you're talking about is actually some sort of subjective feelings being hurt, not really taking offense), Kaepernick and Nike have a lot more cultural power than a few concerned consumers. The way they behave is more noteworthy than a few people on the internet.
Finally, and probably most importantly, it isn't uniformly "dumb" to be offended by something. This is part of what I was saying above, but certain decisions and actions are more impactful than others. Kaepernick clearly has the power to bend the ear of major corporations, which have the direct power to keep products off the market. Probably more important is the indirect power corporations have to influence culture, policy, and other businesses. I don't think this whole thing over the Betsy Ross flag is a huge deal, but I also don't think what Nike is doing should be ignored as another example of radicalism influencing big business. It would be a shame if big business were to convince people that the Betsy Ross flag was something to be ashamed of, so people ought to speak up rather than letting them control the narrative.