Currently, Gaza is dependent upon Israel for everything. With the opening of the Rafah crossing, this dependence will decrease. With an open sea access, (subject to arms inspection) this dependence will decrease significantly. It will also allow Gaza to function like a nation rather than a refugee camp. Israel feels threatened by these things.
Palestinian man suffers light wounds from rocks thrown by Jewish men in Jerusalem (Haaretz)
from the article: Israel prepping to block next Gaza flotilla