How do I protect myself from bad contracting jobs?
Comfort level, commonsense and walk away is about all you've got on your side. Yes, services like Home Advisor and Angies List do have some pull, but if the contractor's gone bad then those services can't reason with them.

First off, don't give any down-money and cancel everything with that contractor. Short jobs of a week or 2, by good contractors, will only require payment or start of payments upon completion.

Longer projects of a month or more, with a good contractor, won't require money until demolition is done and a discovery of any obstacles is discussed and planned with the "estimate" being converted to an "Invoice" with an updated Contract...if needed.

Then, the written Contract will spell-out the agreed payment schedule with goals achieved by the contractor before another payment is made or the establishment of a payment plan or financing. A payment schedule should start with no more than 25% and a payment plan should be no more than 10%.

Once the money is fair and square, then you need to possibly force constant communication and take an active interest in the project. Ask how things are going, ask to be shown any problems and ask about sub-contractors or materials that were to have shown up.

If things change and the project is falling behind, communication ceases, work turns sloppy or daily clean-up stops. Then, stop everything and calmly discuss your concerns before the whole crew (if any). Yes, you may have to take off from work to address the changes you're noticing.

If you're met with attitude from someone you thought you had a good relationship with and nothing's getting re-planned nor resolved, then fire them and provide a partial next payment. You must always be prepared to have another contractor take over regardless of project delay.

This is your money and your home or business and he, she or they better shape up back to how it all started or it's time for them to ship out, period. Building Inspectors, the BBB, Lawyers and the contractor's Insurance Company won't and don't act or do any good until there's gross rubber-stamp negligence.

It's always a gamble and the pressures of any work can get to anyone. But, a professional will re-group, slow down and re-trace or apologize and thank you for picking up what they dropped and get things right back on track. You act professional and they'll act professional.

Don't get paranoid and do realize the stage or phase of the project before jumping to the worst your mind can imagine. Observe, take pictures and notes and give it a day or 3 to correct itself. The contractor and crew want to hear your interest in their process and your praise of their work, but whining and complaining will kill their morale.