The viewers know quite well that since Cersei was involved in Bran's attempted murder. Her statement that she would pray as hard for Bran's survival as she did for Robert's baby will thus give the audience (who haven't read the books) a clear idea of how much she hated Robert's baby. Since Cersei would be praying for Bran's death, it points to her actually killing Robert's child.

When we later hear about all Baratheon babies being black haired, I think Cersei's first son will probably be referenced, allowing to viewer to figure out that Cersei killed the child (with the same poison that killed Jon Arryn, which would tie the disparate arms of the conspiracy).

I think it was also a decent way of showing that Cat was politically quite shrewd. Based on the first episode, and her grief for Bran, this was hardly obvious. But here we see her accepting the Queen's assurances of goodwill, but not hesitating to associate her with the attempt on Bran's life. I think this was a crucial point to make, since otherwise, Cat's later political coup's would seem weird to the viewers.