Qassam rockets are really small, for an anti-missile system track them and shooot them down is hard work, but thats different when it is about large missiles, even more being launched from Iran. The Israelis would know with a confortable timetable where to those missiles would be heading to and could take the necessary measures to make sure the Iron Dome shoot down as much as possible. Yes, as much as possible, the system isn't perfect, like any other system in the world, it will never have a 100% sucess rate.
10 arrested at Israeli Arab protest in Ramle (Haaretz)
from the article: Behind the scenes, both Israel and Hamas want violence to end