Most humans need rituals. I do. Weddings, funerals, baby showers, graduations - these are highly symbolic events that give us a very public outlet for emotions, something most humans very much need. I appreciate that outlet, as do most Atheists.
I recently attended my beloved grandfather's funeral, and while I didn't at all mind that it was officiated by three Christian ministers - he was a religious man, from a religious family, it was entirely appropriate - I did mind his minister opening his remarks with, "We are gathered here today, as people of faith, to..." I sighed and stared at the flowers.
If someone says something to me one-on-one, or in a small group, that implies I'm a Christian, I will correct them. It makes people uncomfortable, no matter how hard I try to be nice about it, but I have to do it - I have to be honest. To not say anything is dishonest.
But in that moment at my grandfather's funeral, there was nothing to do but sit quietly and have my own private, internal tribute to my grandfather for a while, until words were said that made me feel welcomed to be there.
It's not the first time this has happened: I attended a Catholic wedding where the Priest said repeatedly, "We are gathered here as Christians to..." and "Now, let us bow our heads, as Christians, and pray for..." He not only made the Atheists know, in no uncertain terms, that they weren't supposed to be there, he also made sure the two Jewish couples in our row would also feel profoundly unwelcomed.
I have no problem with religiously-lead ceremonies, but I do have a problem when religious leaders assume everyone at a ceremony is a person of faith - and even the same religion. The idea that Atheists have compassion or want to show public support for people they love is beyond their understanding. I don't know how to change that - but it most certainly needs to change.