There are times you, as the home owner, can come out ahead if you're willing to accept the risk and sign a time and material contract. If a contractor is accepting the risk then he's likely to add a contingency that he hopes to not use and will be pure profit for him if he doesn't.

On a large project, it's often better for the Owner to get a quote and sign a contract for that quote (well, multiple quotes and then choose the best one). It encourages the contractor to waste not and to finish on time. You've really got to trust the contractor to sign a time and material contract.