Problem isn't necessary nielsen ratings, but the slot they've aired SGU in. SyFy destroyed their tried and true Friday night slot and started pissing about moving things around so they could show wrestling. As such, the people who watched it tended to record it. This happens a lot more these days. Doctor Who in the UK for example. The first episode had the lowest overnight ratings for a DW season opener since its return, but after the consolidated ratings came, it added over 2 million viewers (repeat viewers aren't counted in this) and came to be one of the more successful ones.
The way people watch TV shows has changed, especially in regards to science fiction and when channels fuck around with when they air shows. Unfortunately, stations in America don't really count these