Every time a show changes, they lose viewers. DS9, VOY, and ENT all had their highest viewing rates at the beginning of their runs. ENT tried to shake things up a few times - at the beginning of seasons 3 and 4 - and paid for that with an early cancellation.
Stargate Atlantis started out much less popular then SG-1 - even if their viewing numbers were about the same, SG-1 nearly always won the "which show do you like better" polls - both here and at Gateworld. It's taken years for people (including me) to admit that Atlantis is actually pretty good.
Overall, people just don't like change
. The public outcry when Ploto was de-planetized is another indictation of that.
Like it or not, BSG has changed a lot over the break. It was never a happy-go-lucky show, but it was clear from the finale of season 2 and opening of season 3 that it was going to be a very different show - less sex and more commentary on the Iraq war (or whatever you want to call it).