It's not really a problem inherent with Goodman product though. Many other brands are distributed at the wholesale level (ex Keeprite, Ducane, Payne, Luxaire, etc). What most consumers don't appreciate with that survey is Goodman is the only wholesale distributed brand listed. Therefore it isn't really a fair comparison.
The Carrier, Lennox, York brands are dealer distributed meaning the manufacturer selects a contractor in a market to represent their brand. Usually these are the better contractors, thus lower installation problems. Consumer Reports includes Goodman in their survey because Goodman is the number one selling brand in all of North America.
Most contractors choose Goodman because of the value and quality of product. However, as Munchos said, this will inevitably include the dubious contractors and that's where the problems start. The furnace manufacturers are similar to the auto industry in that most of the internal components are made by others (i.e. Honeywell, Emerson, Copeland, etc). There isn't anything in a Goodman product I'm aware of right now that one can point a finger to and say, "aha!"
As a company, Goodman is very new. Carrier, Lennox, York are hundred year old companies and are synonymous with the industry. As elnlady mentioned they began as family owned operations. Mr. Goodman began making equipment in the early eighties and now has the number one market share in the entire residential market. Not bad, eh?