Logo is a credential item in a website. Now since you had asked people to look at it and found people are not looking at it (whatever ways of testing involved though), I would reverse the way you tested it. Take the logo out of the webpages and ask them to browse through or do a corridor testing.
Take these sites or anything of your own in two different realms -
1. Sites which people had seen and browsed more often and 2. Sites which people rarely seen and does not have a hang of it.
Look at cleartrip.com, zillow.com, pepsico.com. If you take cleartrip, without the site logo - the user will really be not mentally aligned with the site, since its the persuasion, emotion and reliability of a site is gone for a toss for sure - since being a plain functional site. On the flip-side if you take pepsico, user will still relate to it by the way of richness and graphic of the site. In both cases the users would want the necessary logo placement in its place which is just alike the dashboard in a car - where you never keep watching the speedometer while you drive. As a known functionality - you glance it through to check if its working, which is quite the way it is with the logo. You need to have it, but never always demands its own attention, until its required!
When logo is missing - user will react very strongly - since its the base or identity for a site, User wants to be in a world of direction, identity and know-how. In that event, missing logo's will create lostness factor and the need is always understood - when you remove the need and make user move through. Since you had it on the page - user will always had a glance at it and felt they are there for a purpose. It does not shout - but its placement itself creates critical balance to the design from a universal stand-point.
Verdict - They have not failed to look at logo but they have adjudged and consciously deselected their sensitivity when required. They look at through peripheral vision as extension of other components on the site to form a reality check.