Yes, you get paid when people click on your ads ... just be certain you don't click on them yourself or Adsense might drop your account.
Also, Hubpages gets 40% of the clicks ... the other 60% belong to you. However, when you look in Adsense, the clicks you see are all ones you get paid for.
As for using other affiliates, the only ones supported directly by Hubpages are Amazon, Google Adsense, Kontera, and Ebay. You will also sea Analytics on the affiliates page, but it's not really an affiliate market ... it's a means of tracking your adsense a lot more deeply, to discover which pages are getting hits, how much they are making, and what people are searching for when they find your pages ... a very valuable tool.
I hope this helps. :)