That's a gender inequality thing; you see it in Japanese businesses, too. A man will call a woman of equal position [surname], and a woman will call a man of equal position [surname]-kun. It's slightly more polite, which is why you see women using it more than men.

Among male friends, you see -kun, that's when it becomes a dimunitive. That is, a guy using -kun on another guy, you can take to be mildly affectionate (or friendly, rather). But when a girl uses -kun on a guy, unless they are friends, it implies more that she's being polite than friendly. A girl using -kun on another girl is also better taken as "standard politeness."

In X, Seishirou uses kun on Subaru; this is more condesending than friendly, though, considering their past history - it's the exception to the rule. Consider calling your enemy "miss" or "mr."