Logos are fully customisable, and unlike skins, they take up only a few kilobytes of space, so your opponents need not have downloaded your logos to see them.
Logos have their varying uses, whether to mark territory, advertise a clan, or just to show off.
Half-Life comes with only a dozen or so logos, few of which are interesting. Most people will want to use others. Logos R' Us , run by PHL's very own AutoMag, boasts over 1,300 logos, catering to a wide variety of tastes. His site was doing quite well averaging over 50,000 hits a month, but unfortunately the network on which hosted him shut down. He set out in pursuit of a new venture, and eventually found his way to PHL, where he started doing news.