1) Richard Dawkins's primary contributions to the field, such as 'Selfish Gene', made few reference to religion, which were not in a negative light. Granted, Dawkins has spoken quite aggressively against religion in other contexts, but to assume that his views are concordant with those of all (or even most) other evolutionary biologists, or with the everyday teachers in real science classrooms, is deeply inaccurate. In fact, many evolutionists resent his behavior - not necessarily because they embrace religion themselves, but because the evolution and religion don't usually belong in the same conversation, and certainly not in the same classroom.

2a) Whether or not he was referring to evolution in general, or to evolution by natural selection in particular, is not easy to discern because he used the word "theory". Either way, his message is correct. That evolution occurred is a fact. That the theory of natural selection works is undisputed among people who actually study this subject (and other people who don't study this subject professionally but are willing to honestly address it), both theoretically and empirically.

2b) Think again about gravitation. That gravity exists is indisputable, just like evolution. As to what causes gravitation - we have only theory, albeit very strong and well-supported theory. Guess what? The state of affairs with natural selection is similar: it is a theory regarding what causes adaptive evolution to occur, and it is supported by a massive amount of evidence. I think the NY Times author's comparison is pretty tight.