People might draw the connection due to the idea of a small group (like Noah's family) being set apart in a world full of chaos. In Harry Potter, Harry, Hermione, and Ron form a small group that stands against the forces of the Dark Lord in a world full of dark magic. However, this is just one aspect and the overall story of Harry Potter is much more complex and distinct from the Noah story.
Some might think so because of the theme of a 'chosen one'. In the Noah story, Noah was chosen by God to save the animals and his family from the flood. Similarly, in Harry Potter, Harry was the chosen one to defeat Voldemort. But this is a very basic similarity and doesn't really make it a fanfiction.
The thought could come from the idea of a new beginning. After the flood, Noah's ark led to a new beginning for life on Earth. In Harry Potter, after the defeat of Voldemort, there is a new beginning for the wizarding world. But this is a tenuous link at best. Harry Potter has its own rich backstory, characters, and magic system that are not borrowed from the Noah story.