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The atheist is without God but not without faith, for today he puts his trust in the investigative method known as science, whether he understands it or not. Since there are very few minds capable of grasping higher-level physics, let alone following their implications, and since specialization means that it is nearly impossible to keep up with the latest developments in the more esoteric fields, the atheist stands with utter confidence on an intellectual foundation comprised of things of which he knows nothing.

You don't need to know high-level physics to understand the scientific method. If people needed to know high-level physics to understand science, we would have never learned even low-level physics.

There is a difference between faith in something without evidence (FAITH) and an understanding of the scientific reasoning (REASON). This is not to knock faith, but it is very different in nature from reason. Faith deals with "revealed truths," whereas reason deals in things we can see for ourselves.

We can devise experiments to learn about the properties of matter.

We cannot devise experiments to learn whether or not God really thinks homosexuality is a sin. We just have to go with what we think the revealed truth is (and different people believe differently on this subject, even if they accept the same version of the Bible (the same revealed truths)).

Scientists might disagree on certain things, but eventually they come to agreement. The same is NOT true about religion, because it deals in revealed truths.

Revelation and reason are fundamentally different. Understanding the difference between the two is one of the key tenets of Western philosophy.

whereas reason deals in things we can see for ourselves.

I disagree with this. You may intend to mean "science deals with things that can be measured," which I would agree with.

Reason, to me, describes the thought process by which we deal with data in a premediated, organized fashion. Most of this data, I'd argue, does not come from a direct sensory source.

You read a book about Caesar you will acquire data which will lead you to a conclusion via reason. Yet, you will have never directly "seen" Caesar.