I hate this practice myself (advertising cheap flights that don't show the extra charges--including taxes). I also hate vacation package sites that give you cheap vacation packages, but that require 2 or more stops enroute, that have long layovers (including an overnight in some cases), and that take you way out of your way to get there. Then you find out that switching in a decent flight boosts the price by an extra $300 to 400 or more for a couple to take the vacation package.
As a result, I just won't use sites once I see they do this. This is why I use sites like kayak, travelocity, expedia, and the mamamoto (or something similar) that travellerspoint suggests.
These sites are very clear. Piecar is correct--it is just a bait and switch scheme these other sites use.