What happened is that Microsoft bought Skype, and it clearly feels that of the two brands, Skype is the more valuable (for what they paid, it better be). Having two brands of instant messengers (and two code bases, etc.) with the same target market is redundant, so one of them is being retired.
Google was very smart to tightly (and smoothly) integrate its chat service into its mail service. They did an excellent job leveraging a successful product to turn what was basically a me-too product into another very successful product. Ditto for Facebook, I guess, although I think they were actually pretty late to the game, considering how obvious a fit it was.
Not least because it became more and more obnoxious. It was a very self-important little IM.
Windows 7 automatically logs into Messenger if you follow the default behaviour and associate your hotmail account.
I'm still not clear what scenario has you logging into Messenger automatically on Windows 7. Were/are you running the Messenger client? I'm not aware of any Win7 SKU that shipped with Messenger. That's part of Windows [Live] Essentials. Maybe some OEMs shipped with this preinstalled? I don't recall Windows 7 by itself ever asking me to provide it with my LiveId/Microsoft Account.
Besides, its popularity was, like everything else, depending on countries. When I was a teenager in France, nobody had ever heard of Yahoo! or AOL IM. Everybody was on MSN, with ICQ a far, "geeky", second.
Who knows why none of the IM products expanded into social networks. They basically did what facebook did well before facebook existed.
For example, see here: http://blogs.msdn.com/b/mayurk/archive/2005/03/22/400685.asp...
In 2005, the contact limit was doubled to 300. There are probably hard technical reasons why they couldn't have social networks like twitter and facebook do today.
I don't think AOL, Yahoo Messenger, Gtalk or Google+ hangouts, FaceTime are making any money(if they're not losing money i.e). Notice how each one of them is owned by a megacorp and is/was part of a bigger ecosystem that subsidizes it.
I even wonder if Skype is a viable business by itself, though they have Skype credits for calling regular phones.