The story might be getting darker and more tense overall, but as far as the MPAA is concerned, Half-Blood Prince is actually less scary/potentially objectionable to children than the previous two Harry Potter installments (which were both PG-13). Huh.
Sure, Ron's hookups with Lavender expose us to a whole bunch of what the Brits call "snogging" (that's kissing, Yanks), but beyond that, the "sexual" content is pretty mild.
Things are quieter on the blood, guts, and violence front as well. There aren't too many battles going on (other than mentally?), and there's no Lord Voldemort (only flashbacks to his much more innocuous kiddo self).
So, all things considered, it makes sense that this particular film yielded only a PG rating. Stuff got kind of deep and cerebral in this film. But we're back to PG-13 for the big finale in Deathly Hallows (Part 1 and Part 2), though, so brace yourself.