Google Analytics Reliability Doubts

There is an interesting post at SEOmoz.org called How Reliable is Google Analytics? by Michael Martinez. Michael makes a very strong point that Google Analytics may not be as reliable as we think it is. He compares some numbers between Google Analytics and his own web log data for one of his web sites (Xenite.Org):

For July, Google Analytics says the same page received only 700 visitors and 900 views -- but my server logs indicate over 8,000 views.

The discrepancies vary across the selection of pages. For Xenite's home page, we show over 12,000 views in January but Google shows 2200. In July, Google thinks we only received about 800 page views on the main page. Our server logs indicate 3,000. Maybe the robot filtering doesn't work the way I think it should on my server logs -- I have changed statistics programs enough through the years that I occasionally get a little confused about how to interpret the results. But these kinds of discrepancies just don't make sense.

Our server logs indicate we had 97,000 visitors in January and 81,000 visitors in July. So while a greater proportion of our summer traffic comes from non-Google sources, we didn't lose almost 50,000 visitors -- which the Google Analytics data suggests we should have.

I've been with Google Analytics myself since as early as I got a beta testing invitation before it went public. I liked all the bells and whistles and still running it on all of my web sites, but I noticed, I haven't looked at the Analytics stats for at least a couple of months now - instead, I'm using desktop based software that parses my web logs. I never questioned reliability of Google Analytics directly, but I noticed that the data was very different from the one I was getting myself and somewhere at the bottom of my mind I didn't trust the GA numbers. So I keep using the desktop based web log analyzer. That's why this article was really interesting to me and it really raises good question.