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He says it like it's a bad thing.

It certainly can be.

Militancy: the view that it's OK to tell people that they are wrong.

This would be OK if the people to whom they were saying this to were actually wrong. The truth is quite often they don't have any evidence for this. For example, if a mystic were to go to the average physicist and tell them that they were God and they had created the Universe, they would laugh in the mystic's face, yet that doesn't mean the mystic is incorrect, it just means the physicist did not understand the mystic, nor were they inclined to attempt to do so. This sort of militarism is a block to knowledge and understanding.

Reductionism: the expectation that what things do is explained by what the things they're made of are doing (what else would you expect - some sort of soul that imparts unexpected properties?)

Reductionism assumes that fundamentally everything is made up of individual parts, a "lego-theory of the world" if you will, yet this is not what the known physics itself says is happening. Take the case of quantum entanglement, you have two "things" that yet act as one. Physicists are still baffled by this. Legos do not behave this way.

Further, it must be acknowledged that even if everything is made up of "individual parts", these parts interact with one another, and hence they are not truly individual and separate, their behavior and any meaning that can be attributed to them requires the simultaneous acceptance of all other parts of the system, the understanding of mutual-interdependence (a mystical concept). Without the rest of the parts, the individual components are without meaning themselves. Meaning only arises out of the relationship between the various components, and that does not fit with the reductionist viewpoint.

Atheism: the view that gods need explaining as much as anything else.

No, atheism is the outright rejection of the idea of God. It is a religious belief in itself that requires a faith in the non-existence of any sort of God. It does not ask for an explanation of God, for if it did it would have to accept the possibility of a God.

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Atheism, in a broad sense, is the rejection of belief in the existence of deities.[1] In a narrower sense, atheism is specifically the position that there are no deities.[2] Most inclusively, atheism is simply the absence of belief that any deities exist.[3]

A deity[1] is a postulated preternatural or supernatural immortal being, who may be thought of as holy, divine, or sacred, held in high regard, and respected by believers, often religiously referred to as a god.