why does atticus think it was acceptable for the children to be at the trial

Initially Jem and Scout attend the trial without Atticus knowing or approving. They sit with Rev. Sykes in the "colored balcony" remaining until Calpurnia comes to court looking for them. Although Atticus scolds them at first, he concedes that they have heard enough to be able witness the rest.  

Well, you've heard it all, so you might as well hear the rest.  

I think that Atticus also wants his children to see the darker side of human nature and ignorance that exists in their own town.