The blockade of Gaza is an example of indiscriminately punishing a massive population for the acts of a few individuals. These forms of collective punishment are rightly illegal under international law, and thus the people attempting to lift this blockade were justified. Since they attempted to remedy an ethical wrong, their intentions should be considered good.
The protesters on the flotilla to Gaza had the intention of causing an international media and political incident - humanitarianism was a distant third in their mind. The flotilla was simply trying to land in Gaza as a way of sending a message about Israel, and the Israeli government's action only helped their cause. Regardless of the effects, the aid the protesters carried could've been delivered in many other ways (contrary to many reports) and was an afterthought overall.