Sean Carroll at Cosmic Variance has an excellent post on faith that includes this explanation on how faith can be misleading:
...Here, as I see it, is the problem. Any time we have beliefs of any sort, we need to admit the possibility that they are incorrect. Even if we have think that some result has been reached by nothing but the application of pristine mathematical logic (e.g. the ABC conjecture), it’s always possible that we simply made a mistake — have you ever multiplied two numbers together and gotten the wrong answer? Certainly in an empirical endeavor like science, we recognize that our theoretical understanding is necessarily contingent, and are constantly trying to do better, via more precise and far-reaching experimental tests. These are methods of reaching knowledge that have built-in methods of self-correction.
So what about faith? Even if your faith is extremely strong in some particular proposition, e.g. that God loves you, it’s important to recognize that there’s a chance you are mistaken. That should be an important part of any respectable road to knowledge. So you are faced with (at least) two alternative ideas: first, that God exists and really does love you and has put that belief into your mind via the road of faith, and second, that God doesn’t exist and that you have just made a mistake.
The problem is that you haven’t given yourself any way to legitimately decide between these two alternatives. Once you say that you have faith, and that it comes directly from God, there is no self-correction mechanism. You can justify essentially any belief at all by claiming that God gave it to you directly, despite any logical or evidence-based arguments to the contrary. This isn’t just nit-picking; it’s precisely what you see in many religious believers. An evidence-based person might reason, “I am becoming skeptical that there exists an all-powerful and all-loving deity, given how much random suffering exists in the world.” But a faith-based person can always think, “I have faith that God exists, so when I see suffering, I need to think of a reason why God would let it happen.”
This general line of thought is certainly worth including in any discussion with folks that promote magical thinking.
Update 1 - Cosmic Variance commenter Neal J. King had this little gem to contribute:
Scientific knowledge has to be self-consistent.
Faith-based knowledge has to be emotionally satisfying to the individual.
As long as the faith-based knowledge is not inconsistent with (has no intersection with) the scientific knowledge, who, aside from the individual, has to care about it?