It's misleading if you don't know what it refers to - it makes one think it pertains to something that they need to be aware of, perhaps even something dangerous... maybe a security issue or something like that.
I guess Nielsen is aware of this issue. “Alertbox” is the only headline on his start page (save for the actual title of the website) that has a subtitle: “Jakob's column on Web usability” – a quite succinct description of what the Alertbox actually is.
Calling it Alertbox is certainly more about branding than anything else. (People don’t read on the web; the subtitle is not going to help much, right?) Nielsen has been writing his column since 1995, renaming it “Jakob’s blog” or “Jakob’s column” or something like that at this point in time would be extremely stupid.
Everyone who was somewhat interested in usability during the last decade knows about the Alertbox (if only because they were annoyed by it). It’s a brand. All the noobs (who this website isn’t really targeting anyway) get the subtitle.
It was noted by Amy Schade during the 2008 NNG Usability Week conference that "Alertbox" would not be a wise choice if selected now but that the branding is too strong to support an easy change.
