I wrote for Ars for a brief period, on Linux topics. This was prior to the digg exodus. As a writer, I got a set rate for each page of content, with an expected average word count per page. I'd get a bonus anytime my story hit the front page of digg, slashdot, or similar aggregater. It happened a few times.
But that bonus incentive meant I was encouraged to specifically write stories that would resonate with those audiences. It wasn't fraud or a scam -- it was free market economic pressure. But the effect was the same -- I was tailoring my content to maximize aggregator exposure.
I began to submit my own stories to Slashdot and similar, because a minute of my time could pay me $100 or whatever.
I am not sure that reddit is biased towards these publications as much as they are likely intentionally gaming the algorithms, and encouraging their writers to do the same -- write content you know will hit the frontpage. I don't think it is wrong necessarily, but it certainly isn't organic.
That said, Ars generally has very high quality content due to some very good reporters. Eric Berger comes to mind. So it could be both effects: quality and gaming the system.