In my opinion avoiding a bad experience with a contractor requires good due diligence, preparation and a carefully written contract. When you find your property and begin your contractor search, you should make sure you get recent references and actually speak with them. If you are doing a full gut rehab. you should have plans drawn with specifications. If I am spending 75k or greater on renovations I want to make sure that I have plans and specifications detailing the quality of the materials and the fixtures. An architect adds an expense to the job but as I have learned is essential to getting the finished product you are expecting. If you are using a good contractor than he should take the architects plans and specifications and give you a quote that is binding unless you change the scope of work or materials.
If you are buying light rehab properties you must be familiar with the cost of replacing a bathroom and kitchen, painting, drywall and flooring. Your contract should specify the grade of the materials and on the important stuff actually designate what you want. All of this takes time but it prevents the inevitable dispute at the end of the job when the contractors view of what was required differs greatly from yours. Make sure your original inspection and scope of work covers all of the renovations. You will always come across unanticipated problems. Make sure you understand what needs to be done and enter into a written change order with the contractor before he does the work.
If you agree to a fixed price quote based based on a detailed scope of work, you should not care how the contractor makes his profit.
On smaller light rehab. my partner who has a full time job and extensive general contracting experience runs the job and he splits the profits. He provide receipts for all of the materials' and we use tradesman at night and on weekends who want to pick up spot work. That is how we control the costs on those jobs. The more you know the less likely you will be scammed by a unscrupulous contractor. Good luck!