Might be because an omni has a beam pattern like a "donut". You will always get bad signal if located BELOW an omni, because omnis (if not tilted, which I would consider a really strange setup) will transmit/listen in (more or less) a "plane" around them.
Apart from that, there are several others factors that could come into play.
For example: What's the material of you roof? Does is let RF through?
With your setup (hig gain omni on the roof-top) I would suspect that you will/could serve internet to lots of your neighbours quite well, but probably not for yourself
Best regards,
Christian Meis