They're not using the current flag. They're using the flag from a time in this country when slavery was still a thing and I believe that the point of the backlash.
Everybody needs to take a step back, a deep breath, and look at what the internet is telling them to be upset about this week. Unless the flag code doesn't pertain to past flags, people should be upset that Nike was planning on doing this in the first place, not that they decided to pull them. However, most of those people are hypocrites and will be rocking American flag cargo shorts during the 4th. Also, let's not pretend that Nike was this US-made apple pie company up until yesterday or whenever this happened. Were all these twitter patriots planning on buying shoes that go against the flag code, has you walking on the flag as it's on the ground as part of your shoes, and is made in some other country? Seems odd to me.