If my memory serves me right, GNP includes all the "types" of commerce (beakers, gold, culture, espionage). I believe the raw commerce itself is never counted. So a civ with lots of wonders might have a high GNP simply from generating a lot of culture.
If you ever keep an eye on the GNP graph when "binary teching", you'll notice the GNP keeps going up and down over and over. That's because when you have science at 100%, and assuming you have more science modifiers in your cities than gold modifiers, you'll produce more beakers in those turns than you produce gold on the turns when science is at 0%.
Having said that, cottages are a good way to increase your GNP. But any other income source is just as likely to increase your GNP graph. e.g. specialists, esp producing buildings, ...
One thing in particular that doesn't factor into GNP is the beaker count from bulbing.
If you bulb a lot of techs with great people then it might be ok to have a lower than average GNP.