Which means that Amazon gets a big unfair advantage vs. local stores.
What's unfair about it? They're not consuming any resources within the state, like Brick & Mortar merchants, who have an advantage of their own - physical stores to bring people in and sell them stuff on the spot.
Wouldn't that mean that brick and mortar folks are being doubly taxed? After all they are paying taxes to maintain that infrastructure in addition to what Fedex and the like are paying.
The Quill decision was largely premised on the lack of contact between the catalog company and customers in the state--that is, such contacts were so infrequent (i.e., less than double-digits a month) that it would be unfair to impose any sales tax obligation on them (the "substantial nexus" requirement). The same cannot be said of Amazon; it regularly sells to hundreds, possibly thousands of (insert state here) customers each day. This is more than sufficient to establish a sufficient nexus to Colorado so as to justify the imposition of a sales tax.
Note that if you read the decision, the key issue is not whether a state can impose a sales tax on out-of-state retailers (it cannot, even without physical presence, if the substantial nexus test is met), but whether the state law unfairly discriminated against out-of-state retailers (which it does, the law is poorly written).
The reason Amazon folded against New York and California is because it knew both states were willing to take this all the way to the Supreme Court, and it knew that if that happened, it would lose.
What's unfair about it? They're not consuming any resources within the state, like Brick & Mortar merchants, who have an advantage of their own - physical stores to bring people in and sell them stuff on the spot.