First of all the posters assume they actually speak for all natives, which I find unjustified. They are one group of natives who happen to hold a certain set of opinions, as entitled to them as any one. The reality, in the same gist as the people who have complained about the use of "master" as Git name, is that they are a loud but irrelevant minority holding an opinion on a matter that has no benefit to anyone.
It is also apparently implying that any idealized representation of a minority group constitutes "erasure", as if certain cultural stereotypes were a sin. Every idealized telling of a story is going to omit details and be reductionist; every outsider perspective of a group will have some sort of stereotype because there are hundreds of minority groups out there and nobody has the time to engage in a deep investigation of each. That doesn't mean idealizations are bad, or negative, or actually useful if they're going to be retold in a historically precise manner (symbols need to be reductive to be useful in idealized contexts). Symbols are symbols; the rationale for the name is interesting and innocent.
There's this awful trend in American minority militants that seem to get worked up about truly innocuous causes and stereotypes that are harmless, and at their very worst naive. As someone who's been around groups that have fought and resisted serious minority causes, it just shows their powerlessness and inability to fight for actually useful causes. It's just a huge waste of their breath that shows their lack of credibility.
Imagine if this were the "Irish Software Foundation", named because a guy watched a documentary on the Potato Famine and thought Irish people seemed noble and hardy. Of course that would be offensive and stupid.
Speaking of which, a lot of minority identities actually do revolve around certain set of values like the ones you mention.
People stereotype people all the time. The fundamental causes of distress of the indigenous people in the US have approximately zero to do with that.
Mazda is a car manufacturer, however, it also the name of a god.
Pick any technology name and it will have a double meaning in a language or region in the world.
Where do we stop?
It would be more meaningful if the Apache foundation included a link on the homepage explaining the origin of its name and an make an annual contribution to a relevant charity.
Companies regularly rebrand. A brand depreciates, just like equipment, and so is regularly updated.