Personally, I think part of the problem is the assumption that Work X is so unique, that no one thought of it before Work X, so if Work Y has similar elements, it must have been influenced by Work X. Which strikes me as a logical fallacy.
For example: looking at Books of Magic, it has a physical similar hero to Harry Potter. But so does Simon, from "Simon in the Land of the Chalk Drawings" from the late 60's/early 1970s. A slight boy with black hair and big glasses is hardly a unique visual aspect. Nor is the idea of a boy who grows in obscurity, ignorant of his true heritage or powers. Especially when you consider the plot of Books of Magic is mostly just an excuse to do a whirlwind tour of the DC Universe's magical characters...Tim Hunter is as much literary device as actual character. And let's be honest, here: Books of Magic, popular as it was, did NOT reach a huge audience. It was a COMIC BOOK. A high-priced, well-written and beautifully illustrated comic book, but still just that all the same. I think it's safe to say that Rowling is much more likely to have read (or watched an adaption of) Tom Brown's School Days than The Books of Magic.
Many of the themes and elements that Rowling draws upon are common fantasy themes and shared literary references that plenty of authors use. Harry Potter owes as much to Gormenghast as it does to Books of Magic.