As the affiliates page says that you earn 10% of the impressions, yes you earn from them (hopefully). The reason its less might be because of the 10% share of the impressions. I don't know what traffic your referrals get but as you're saying that you should be earning a lot more, I guess you've referred some high quality writers. But all the traffic their hubs get don't have HubPages ads shown in them.
This is because HubPages uses a third party program called YieldBuild. If YieldBuild thinks AdSense might convert well instead of HP ads, it shows AdSense blocks over the HP ads. If it thinks HP ads convert well in that session or in that page view, it shows HP ads. So, all the traffic or pageview your referrals get don't have HP ads. Further, the 10% share is really small, so its pretty justified. Hope it helps!