Gomez has had some bad press recently. Yes, they focus on web sites and they sell their consulting services to the organizations that they rate. Objectivity would be very hard to sell when they have these kinds of practices.
Another question about the survey results is who really cares? If you are getting service that meets or exceeds your expectations (as a premium flyer) then a broadly based survey may have zero personal relevance. Yes, it is good to know that you might get pleasant service on XXX Airlines, but when they have only four flights a day to your home airport, then you may be stuck with something else.
There are all sorts of variables that could be attributed to an airline when they are more likely attributed to the system itself. SFO flyers are generally unhappy because their airport does not have the land that DFW and DIA have. On time figures suffer for UAL /Shuttle because of this, people are unhappy and they rate UAL poorly on this factor. At the same time they like UAL's frequency of service--and this might negatively influences on-time figures.
Complaints could be something that describes the kind of passengers that an airline carries rather than the airline itself. AA has better statistics than UAL in most categories in the latest DOT figures, but the passengers at AA complain more often.
The bottom line is that you have to judge and weight things on your own. FT is one way of gathering information regarding airlines, but your own experience might be the best measure.