To be clear, the problem is not that Apple is flagging terms that are most often used in unwanted, spam messages—it’s the lack of transparency about this filtering. Apple is flagging messages that it seems very sure are spam, but it has no real system in place for dealing with false positives—messages that are filtered, but aren’t actually spam.
Apple deletes some of the false positives outright. They never even appear in the Junk mailbox. This has been going on for many years. It’s also no longer possible to turn off Apple’s server-side filtering, e.g. if you prefer to use another filter such as SpamSieve. These days it’s easy and inexpensive to host e-mail on your own domain, and there are free e-mail services that are better than Apple’s, so I see little reason to use iCloud for e-mail.
Update (2013-03-01): Matt Henderson:
I’ve been telling friends and family for years to think twice before using a Gmail or iCloud email address — or even worse, the email address provided by one’s ISP. The problem is lock-in — once the world knows you @gmail.com or @earthlink.net, it’s not easy to change when you become concerned about Gmail account hacking, or when your ISP goes belly up.