I'm more familliar with the diesel world, but I can't recall the last time I heard about a turbo
hurting fuel economy (assuming the turbo match has been done properly).
The turbine side of the turbo captures some of the exhasut energy and turns it into pressure on the intake side (which decreasing pumping loses). In fact, with some particularly good turbo matches, the intake pressure can actually exceed exhaust pressure to the point where pumping losses are completely eliminated--or even reversed (positive pumping work).
Turbine efficiencies in the 60-70% range are pretty common and compressor efficiencies of 70-80% aren't uncommon either--that makes the combined turbo efficiency over 50%, which is better than the base engine. As has been noted before, a "turbo bypass" is called a wastegate. I've tuned them before on diesels. When they start opening, you start losing efficiency pretty quickly. That's actually the whole point of a wastegate--it reduces turbo efficiency to keep the turbo from overspeeding.
Also, as has already been mentioned, turbocharging allows for downsizing and/or downspeeding of engines, which increases fuel economy by allowing the engine to run at lower speeds and higher loads (lower friction, pumping losses, etc.)
Just to make my point further, I Googled "turbocharging and fuel economy an came up with several stories:
Auto industry boosts turbocharger sales to save gas
Top 5 Turbocharger Tech Innovations: The Truth about Fuel-Sipping Turbos - Popular Mechanics
Honeywell Turbochargers Enable 20 To 40 Percent Better Fuel Economy Helping Automakers Reach CAFE Targets
Design News - News - Turbocharging Technology Reduces Fuel Consumption
Today's turbochargers focused on fuel economy over performance - SFGate