Aside from the obvious, which is either a company cashing your check and never doing the work - or - delaying the project because they already have their profit in their pocket...many things are involved in a window project other than just the windows. First, the installers from any company will be literally tearing apart your home. To ensure that your project is done 100% accurately, you should consider many components that most homeowners never even think about.
Questions you should ask regarding the installation:
These are just a few things that will insulate you from ever being up charged for your project, or even worse, having an inferior installation.
Lastly, will the installers be picking up and hauling away all job related debris? What about vacuuming your home and washing your windows?
By not giving a down payment, you have the advantage of knowing that until the project is done 100% correctly, the company you are dealing with will not be paid. This is by far the most potent way of protecting yourself and making sure that your home or your new window project is done in a professional and seamless manner.