The rating is right in line with last season's finale. It is a bit foolish to compare two season premiere's (S2 and S3). I made the same case for Lost.
Additionally, look at the time of year BSG started last year vs. this year. Like it or not, a significant portion of the people who would watch BSG were watching the Yankees/Tigers baseball game. The Yankees are probably the biggest draw in baseball. Even if it only got a 5.x rating, that was still viewers who would might be watching BSG.
Splitting Sci Fi Friday was a bad idea, starting the season in October against post-season baseball and the new season was a bad idea. Hopefully this quashes any kind of talk about BSG jumping to NBC.
Edited to add: total viewers from 2.5 is up, the 25-54 demo is up, the 18-49 demo is up. And it was the #1 cable series on Friday night. The rough 1.8 looks bad, but the numbers did tick up.