But that's the point. These kinds of protections should be enshrined in law and not subject to the whims of the voters. While that is somewhat of a moot point, since the law is basically just a reflection of what the will of the voters wants it to be, it is an important distinction to have made.
I agree in principle. I also think that it's a bit silly to boast about being the first to legalize it through referendum because of it. If a referendum on gay marriage had been held here back in 2001 (when we legalized it), the result would without question have been 'yes'. But since the very first two lines in our constitution read "Everyone who is located in the Netherlands will be treated, in equal situations, with equality. Discrimination because of religion, life philosophy, political orientation, race, gender, or any grounds whatsoever, is forbidden", there was never any real question about a lack of legal gay marriage being unconstitutional. There was no need for a referendum, just people pointing out "hey we exist and we'd like the rights granted to us by the constitution".
That's the ideal situation. Though, of course, when a country's politics is dominated by bigots, they could prevent the application of constitutional laws guaranteeing equality... so it's hardly ideal. Still, a country should not have to extend rights by popular vote when the spirit (or even the letter of it as was the case here) of the law already guarantees it.