Most people do not have the resources to lobby for that sort of tax system. Amazon, and other corporations, do.
EVERY argument about what is "morally right" w.r.t. paying taxes is a matter of perspective. To you, what Amazon is doing is immoral. To someone worse off than you, what you do routinely on your taxes (deducting mortgage interest, student loan interest, etc.) is immoral.
The problem is both. It is a problem that people lobby for selfish policies that ignore the needs of others, and it is a problem that the system sometimes listens to them.