You're really asking two questions: "why do window companies have terrible reviews?' and "what should I do?"
Why do window companies have terrible reviews?
There is no single "best" answer. In the U.S., the "Window" industry has lots of companies, like these:
local fabricators ("We are the factory!"), who buy glass by the truckload as a commodity, cut the glass and put it into frames (usually vinyl, sometimes fiberglass), and have their own installers. These guys often run "50% off" sales", "buy one get one free", and spend tons of money on advertising: billboards, radio, TV commercials. You can probably guess that anything that's regularly sold as "50% off" or "BOGO" is over-priced to begin with, or corners have been cut on quality.
small-time contractors who will install anything. You can luck out and find a good one, or you can find one that will disappoint you.
"Window replacement" divisions of the major national window manufacturers. You should know that "replacement windows" are not exactly the same as windows designed for new construction, and because they have installer crews, the national Replacement Window companies (like the local guys) are "sales-focused" (meaning production and revenue). They are also sometimes run as an "arm's length" division of the parent company, so they benefit from the parent's reputation, but they are more than just a manufacturing company that focuses on a quality product -- they also have to deal with the public (retail), hire installer crews, and compete with the local guys in an industry that's not known for a stellar reputation. These are the companies that will come to your house for a "free in-home consultation", sit on your couch, ask you if your spouse is home, ask you to "sign up today", offer "this week's special pricing", etc.
It may be that you were unlucky and picked "bad ones" to investigate their reviews, but bear in mind, the "barriers to entry" are low. I agree with the comments that "the typical person will only post (reviews) if they are upset"(1). Some people in the comments even say that the whole window-replacement industry is a racket.
What should I do?
If the "yellow pages" / online search method isn't working for you, here are two easier ways to go.
1. Find an independent home store.
Find a lumber yard that sells windows, doors, home improvement items and the like that does business with both the general public and contractors.
If you're lucky, and there are more than one in your area, start with the one that's been in business the longest. Go talk to them. They likely have a few contractors that they refer business to, or an in-house installation department, where they "sub out" to local contractors.
A business with a physical store to maintain will likely have screened their contractors well, and you know exactly where to go if there is a problem.
You may pay a slight premium, but a local business with a good reputation is a very good place to start. You generally won't feel any pressure to sign-up for an installation when you walk into such a place, because that's not their business model (they have folks walking in all the time).
Talk to them about the windows they carry. If you're looking at brand-name windows (in the U.S., names like Marvin, Pella, Andersen, Jeld-Wen), ask them about the different grades (levels of quality, or 'series') and what the differences are. Some of the bigger brands not only have different grades, they get down into the "builder-grade" using different brand-names (like "Silver Line by Andersen").
Tell them what's important to you.
- Insulation R-value.
- Ease of cleaning.
- Whether the screens are on the inside or the outside.
- Exterior and interior colors.
- Whether you want the glass to be as flat and non-wavy as possible.
- Price range you can afford.
- Materials (wood, vinyl, fiberglass) -- if you don't know windows well, especially have a discussion about this.
- How the windows operate.
You should be able to learn a lot about the product, and can come back to them multiple times until you're comfortable. Take their business card and let them know you'd like to come back with more questions. There won't be any pressure to sign up now while a sales person is sitting on your couch.
Source: I've had positive experiences in multiple U.S. metro areas where I've lived going this route (for Windows and other items like bathroom renovations).
2. Go to a national home-improvement center.
I don't always recommend them, but if you are in the U.S. and have one of the national chains in your area (Lowe's and Home Depot), you can always go to the windows department, talk to their people, and sign up with their installation.
Their business model is similar to locally-owned stores -- they have local contractors that they "sub-contract out to" -- but you will be dealing with the store and scheduling through folks that work at the store.
You may not pay the absolute lowest rate, but in my experience you will get a good-quality installation and if there is any disappointment, they will be in a position to make it right. The national names screen their contractors pretty carefully (they have to, they can't afford bad publicity) and require their contractors maintain minimum levels of satisfaction.
My personal preference is to support locally-owned businesses in my community when I can, but if #1 does not work for you, then #2 will give you a good-quality result at a fair price.
Source: Personal experience dealing with the inside-sales desk at both of the national chains.
There is no one best answer to this question, but this should get you moving on your project.