I think the 90% refers to interception attempts, not to the whole number of missiles launched. I read other articles which gave a lower percentage overall.
The article claims that Iron Dome won't fire if the rocket is going to hit in an unpopulated area. They're only intercepting the ones that will hit where people are. The assumption is that it would cost more to rebuild buildings than the cost of the interceptor. Of course the value of saving lives is immeasurable. Overall I would guess that the cost of the system is small compared to the overall military expense. If it is actually cheaper to launch than rebuild the target, this system is actually saving money. The entire operation is probably a sucking sound on the Israeli economy.
The flipside of the 90% interception rate is that Hamas could stop firing missiles altogether and only see their success rate go down by 10%.