It's because the Character of the Day is usually an adult and Ash and co are children.
It's also because the anime in general has scaling issues and fluctuates between being land of the giants and munchkinland with both humans and Pokemon. As time went by they got a little better with scale so not every adult is twice as big as Ash.
Not all of them are. A lot of them are the same height as Ash.
However I think you're talking about those Johto female COTD's. For some reason back in Johto, a lot of the female's were taller than even Brock.
I remember that Trixie girl with the Azumarill who Totodile fell in love with...that girl was huge. She was taller than Brock.
It's also because the anime in general has scaling issues and fluctuates between being land of the giants and munchkinland with both humans and Pokemon. As time went by they got a little better with scale so not every adult is twice as big as Ash.