How is Amazon bypassing 3D secure?

You can elect not to have it if you don't want it, it's actually up to the merchant. You might also notice Amazon in some regions does not even require the CVV.

3D Secure gives you discounts on the processing rate since it reduces risk of fraud. However Amazon gets discounts for its scale and elects to avoid it, presumably to improve conversion - and offer features such as the one click checkout.

It's only mandatory for selected regions, like Europe (PSD2 SCA), but even there the merchant can ask for exemption based on the amount, level of risk and recurrence. Transactions under 30 EUR are exempt by default, unless the customer have initiated 5 transactions, or 100 EUR worth of transactions since they were last authenticated. For recurring fixed payments only the first one has to be authenticated.