Why do churches often have altars? In Judaism, the template had an altar for sacrificing. But we believe our sacrifice is done.

So, what is the point of a church altar?
In Roman Catholic liturgy specifically, the altar is where the Eucharistic Sacrifice is made; i.e., Christ's one sacrifice on Calvary is made present again on the altar at each mass. The altar, in this theology, is still for performing sacrifices.


  "In the New Law the altar is the table on which the Eucharistic Sacrifice is offered. Mass may sometimes be celebrated outside a sacred place, but never without an altar, or at least an altar-stone."


http://www.newadvent.org/cathen/01346a.htm

As the largest unified body of Christians on the planet, Roman Catholics have a large influence on the terminology we use. Note that as a Protestant I don't agree with this theology, but the term "altar" likely persists in our churches merely as a matter of "stale" terminology used by those who do not know better. Protestant theology (at least all that I'm aware of) does not allow for an "altar." The reason to have an altar is antithetical to the Protestant doctrines regarding regeneration and justification and having something that fulfills the purpose of altar (meaning that it isn't just a matter of stale terminology) is nonsense in Protestant churches.