Many atheists oppose the National Day of Prayer, to the point of filing lawsuits against it. In my opinion this is both silly and counterproductive. Here are some reasons, in no particular order, explaining why a prayer day doesn't bother me.
It's generically religious - I know the main backers are Christian, but it doesn't specify or exclude anyone of any religion that wants to participate.For more of my thoughts on prayer, see here and here.
It's a U.S. tradition that arguably has roots in the early days of the Republic.
Most of the country believes in a god or gods.
Prayer doesn't do anything. Since I don't believe in God, I don't care if others want to talk to imaginary beings.
It's voluntary. No one is forcing anyone to pray.
I don't believe it's a violation of church/state separation, because of aforementioned generic nature of the proclamation that can include people of all religions.
Ceremonial deism has been part of the U.S. since its founding. A non-specific prayer day fits in with that tradition.
Protesting or taking legal action based on an extremist interpretation of the establishment clause makes atheists look like easily-offended jerks who can't tolerate any open expression of religion in society.