Yes, she did, but only when she was sure Hermione was treating her sons right. Molly's loyalty was with Ron and Harry first, Hermione next.
-EDIT: Molly loved Hermione, but there was a rocky part when she thought Hermione was dating Harry and Victor Krum at the same time. She read this in the Daily Prophet which was written by the gossiping Rita Skeeter. She was still somewhat nice to Hermione, but she thought Hermione was hurting Harry, so she wasn't very fond of Hermione at all. Once she realized it wasn't true, Molly went back to her old self towards Hermione.
As a concerned parent she made sure that Hermione and her sons got on all right, but then realized that all rumors were untrue and that she couldn't wish for a better friend for her son and Harry