Now mind you, there is a huge problem with many churches teaching things that inhibit the ability to think critically. Atheists when pointing this out are often not wrong. However, I have encountered numerous atheists and other critics of Christianity who by all accounts have stopped thinking critically themselves. The common perception among them is that by being critical of religion (particularly Christianity in the west), they are exercising critical thinking. However, critical thinking implies not only questioning authority and commonly held views, but your own views as well.
Critical thinking has often been popularly described as “thinking about thinking.” Stephen Brookfield is an award winning expert on education and teaching critical thinking skills. Below is his definition of what critical thinking really is.
“Critical thinking describes the process we use to uncover and check our assumptions. First we need to find out what our assumptions are. We may know some of these already (these we call explicit assumptions) but others we are unaware of (implicit assumptions)…. Once we know what our assumptions are, we enter the second phase of critical thinking, that of research. We try to check out our assumptions to make sure they are accurate and valid… The third and final phase of critical thinking puts the first two stages into practice by applying our analysis to our decisions. Decisions based on critical thinking are more likely to be ones we feel confident about and to have the effects we want them to have.”
– Stephen Brookfield
Developing critical thinkers: Challenging adults to explore alternative ways of thinking and acting. (1987, Page 9)
If an atheist wants to be a good critical thinker, and not simply a cynic, I would recommend that he or she would do as Brookfield suggests, and check their assumptions. This might entail opening a book by an apologist that they do not like, such as William Lane Craig or a conservative text critic like Daniel B Wallace, and be open minded that they might have some things right.
Checking multiple sources that disagree with each-other and weighing the evidence in your mind is sometimes tedious, but in the end it is worth it. You will have a more well rounded view. As a proponent of critical thinking, I do not claim that I have all the right conclusions. If I am not right, but I want to get it right.
Furthermore, critical thinking applies to much more that philosophical argumentation, but also to very practical aspects of our lives and what we need to do to get to where we want in life. That is a very valuable form of free-thought.