But given that that's not possible, http://microsoft.website would be better than http://microsoft.com except on historical grounds.
Do you know what "com" stands for? Commercial? Would you believe me if I made a convincing argument that it stands for something else - probably.
As it stands, TLDs are not used for their intended respective purposes in practice (.com for commercial, country codes, etc), so expecting this situation to suddenly change is unrealistic. I would expect, in fact, that the most successful uses of .website will be by smartasses for IRC, email, etc.
If something.website is actually not a website, then things are different. But we live with something.net not being an ISP, and something.com not actually being a commercial entity -- so I can't accept that the new TLDs are that much worse than the old ones? Not to mention the geographical based TLDs... is really "codewith.us" defined by being based in the USA?
Naming things are famously hard, and you can only have one TLD for a single "thing" (Not counting things like att.com for the commercial entity, and att.net for the ISP etc) -- if what you do is run a website (eg: medium, blogger, mypetproject.website) -- I don't see .website as being a particularly bad TLD.
All that said, I do agree with your last two paragraphs.
Similarly, http://ftp.company.com is a bit of a misnomer -- if it was an ftp server, you'd have to use "ftp://" -- but of course a single host might run several different daemons, or a daemon might speak several different protocols.
I can appreciate that for many people "www" and ".com" 'denotes a URL', and also agree that without context, "Something.anything" doesn't really look like an URL. I fail to see how that's a problem within the context of hypertext (where the expected behaviour is clicking a link).
[Ed:spelling]