The Key difference was MS was an effective Monopoly in their market with something like 90+% of the market share
Amazon is big, but still is only about 36-40% of the e-commerice market share, and far far less of the over all retail Market Share which is still dominated by Wal-Mart
The problems Microsoft had at the time went way beyond having IE already installed with Windows. Besides, without IE already installed the casual computer user would have a more difficult time downloading a competing browser.
I'm not sure it is. You start off in a position where you don't have the device, and you either go to website A or website B to buy it (leaving aside details where you already may have an Amazon account).
With the IE case, you start off in a position where you already have a browser and you have to perform an extra step to get a different one.
If MS was abusing it's market dominance then, so is Amazon now.