The lungs are actually not equally effected by cigarettes and marijuana. A recent study found that marijuana does not cause lung cancer like smoking tobacco does, possibly due to the rate of cellular regeneration involved between the two. You do get a lot of harmful chemicals from marijuana, and there are certainly negative effects from heavy smoking (emphysema, possible mental problems). However, unless you are an absolute chimney, you're probably much better off getting high on weed than smoking a pack or two a day. On that note, usage trends also probably make a difference in health--cigarette smokers tend to smoke much more by volume.
I'm not a huge fan of either, but I'd rather people smoke weed than cigarettes, frankly.