I had similar thoughts when I was researching the Payment Icons article (not published yet but coming soon) because the icons basically were just the logo of the service and some artwork around it (sometimes, in many cases nothing but the logo). I guess if the icon uses the logo without modifying it (i.e. replacing the fonts or something) and it’s stated that the logo is trademarked by the company that owns it (not the author of the icon set), this is acceptable.
After all, social sites and payment companies do benefit when their logos are used on third party sites because this is great publicity for them and brings them traffic. Trademark owners definitely benefit more when a site uses an icon with their logo, than when the site adds some text like (Join us on Twitter) without any recognizable branding symbols of Twitter, or when the site doesn’t use anything that mentions Twitter.
I haven’t heard of anybody - a designer or a site master - having problems because of non-standard icons but I am curious to know the legal explanation why this use is OK, if it is, or why not, if it’s isn’t OK.
In other words, even though you might be diluting their brand recognition, as long as it is representing them they look the other way. But if you are using a version of the logo to misrepresent yourself as them or capitalize on their popularity, they would take action.