From reading the media reports and seeing the various personalities on TV, I've got the impression that the fuss about the location is due to some sort of internal power struggle going on within the childrens hospital sector. Whether its the fact that 3 hospitals are being merged into one with resulting loss of empires for some, jealousy over which of the general hospitals has gotten the gig or just the personalities involved or any other reasons I dont know. But it is very clear that the anti-Mater crowd has some sort of gripe that is not necessarily linked to the location.
On the location issue, while I'm not a great fan of the Mater site, it is a lot more central than any of the other locations proposed and a lot better than Crumlin, which is a nightmare to get to. The reports seem to recommend that the hospital be beside a major teaching hospital, which somewhat limits the choice - building a standalone hospital on the M50 is not an option. If this is the case, the alternatives to the Mater are St. Vincents, St James and Beaumont.
And no matter where you build this hospital, it will be convenient for some people and inconvenient for others. For people who live in a lot of places, Crumlin is very difficult to get to and Tallaght is so inconvenient that the hospital might as well not exist. You cannot please everyone.