Yes, yes I have heard this explanation a million times, but it's utter nonsense.
The whole system was designed with what you said in mind. The company is supposed to pay their taxes (foo) AND the city is supposed to collect the taxes from employees (bar). The whole system needs everyone to contribute their right amount so there is enough money for schools, health care, police, roads, libraries, etc. etc.
Yes, Amazon's foo is very large, because they make a massive amount of profit!! Also the bar they create will be very large, because they have a lot of employees. The fact it's a large amount changes nothing. The city they are in needs BOTH of those to function correctly. With all those massive buildings and employees the city will need new schools, roads, more police, more libraries, etc. etc.
Amazon get to use the roads of the town, the water infrastructure, the elec infrastructure, the education, the police, etc. etc. to make their massive profit.
Who do you expect to pay for all of that, other than Amazon through their foo tax? That's precisely why the foo tax exists, and amazon get to avoid paying it they can make massive profit without paying for the basic stuff - so now the regular citizens need to!
The whole thing requires the full amount of foo+bar to pay for all of that stuff.
But of course we all know America has terrible tax-payer funded services compared to the other OECD countries.