I always figured he saw Matt as a nothing as a superhero, but nearly untouchable: Matt's powers don't seem detectable, Matt can always tell when he's being tricked/observed, in the courtroom? Matt is the equivalent of Thor.
Also, he has so much credibility that even as an unregistered vigilante wearing Daredevil's costume allowed Peter Parker to walk right into a station and work with the police.
All of that (and the Hand) make him surprisingly dangerous. But most importantly, DD is Spider-man's kindred spirit. It would be like killing Ben Reilly over again.