I used to be of the thinking that replacing AD with CE really changed nothing, and that what we were doing was changing terminology for the sake of political correctness, but that the calendar is still based on the same event, and that it still is Christian-focused.
Recently, a colleague pointed out to me that CE stands for this code: "This is the counting of years used in our culture, and although we would like to propose a new system which is non-sectarian, that would be difficult and unlikely, so let's use this term to acknowledge that our count is non-inclusive." I think this is best: by not using AD we are showing that we understand that this system is foreign to many people, in terms of their religious belief, and that we're making some concessions in that direction.