They only started making any profit within the last few years, which is why this discussion has started now. For the vast majority of their history, they made no profit or almost no profit at all, which is why they have a low tax bill. The government designed the tax laws to encourage businesses to invest, because investment is good for the economy.
Amazon doesn't have a free pass. They are benefiting from an incentive that was specifically designed to get them to do exactly what they've done. If you change the laws, it would encourage businesses to not invest in the economy, which is exactly what you want them to do.
Except in this case it isn't good for the economy. Amazon's investments coupled with shareholders not caring if they don't make a profit have given Amazon monopoly power which they use to crush their competitors.
No VC will fund a competitor to Amazon. They know any company that tries to fight them will either get crushed or acquired.