Why did it take so long for scientists to find super volcanoes if they are so big?

Because they don't really look like volcanoes and they erupt very infrequently. The Yellowstone caldera, for example, is a big forest- and lake-filled area with some fumaroles and geysers. It does not look anything like a traditional stratovolcano or shield volcano, but after decades of study it was recognized that the caldera periodically has huge eruptions. Same situation with the big lake-filled caldera in Indonesia (can't remember its name, Toba or something). None of the "supervolcanoes" has erupted in recorded history (fortunately) so their eruptive nature had to be uncovered by "detective work".