Reason alone is not enough. It took me a really long time to realize that. And a big part of my journey has been predicated on the idea that reason can conclusively differentiate truth from not truth.
Allow me to stop and clarify, because I mean something extremely specific here: what I mean is that if you were only allowed to use reason, you could only deduce a priori truths. You could formalize logic. You could do a fair bit of math. But that's about as far as you could possibly go.
But surely this is not surprising. All of our modern scientific knowledge is a synthesis of reason and experience- science is itself predicated on empiricism. Empiricism is in fact entirely divorced from reason (in a sense)- our deductions must be verified by experience, not the other way around. We don't theorize about the world based on logic and create laws that apply to nature; rather we observe nature and from that deduce its laws.
But there is one more very real sense in which knowledge does not flow from reason alone. We cannot ever be entirely sure of our own reason. This took me a long time to admit- ironically, I realized it through empiricism. My rationality has failed me too many times to be trusted. My view of the rationality of religion has changed (more than once) over the last five years.
Now I'm definitely not advocating for giving up rationality here. I certainly don't think that we as humans have a more reliable method for determining truth in the absence of direct observation. But I am advocating a somewhat tempered view of our reason. I think atheists tend to glorify reason as a proxy for truth- and I think properly applied reason does lead to truth, in the domains it is capable of addressing. But I'm not so sure how confident we can be in our own application of reason, and I'm not entirely sure as to what that reason-addressable domain is. To put it another way, I think logic and reason are the strongest way we can know truth. But they are not a foolproof way. And they are not the only way.