I think the first and second reasons apply to bookmarkers, and the third applies to publishers. For publishers, the primary reason is the front page IMHO.
"So stuff that goes beyond "please bookmark us" - that's what those buttons do - seems dangerous to me. Especially since actual users have the extension or bookmarklets installed and do not need the site buttons."
I can understand this sensitivity. If you look on my blog, I have a simple link that says "bookmark everywhere." But my popular delicious content is no longer rewarded with a front page link.
"I'd seen an enormous amount of shady behavior in and around this so perhaps I am oversensitive. At one point I was spending half my day, every day, dealing with spam on delicious."
Spam sucks hardcore ass. What else can I say?