Is it a new Nexus? I would expect it to charge faster than that via the mains.
(On a side note, I let the battery on mine go totally flat recently and when I tried to charge it from the mains, the screen went black and little dots flashed up. It took a few attempts of plugging it in and out before it kickstarted the charging into life. It seems to be fine now but I was worried it was totally dead! Definitely won't let it run down so much in future!)
A lot of modern phones that charge over Micro USB seem to have that problem - they need to boot up certain services before they can draw power from it and start charging the battery. Though it does seem that in most models, at least a trickle gets through before that boot level, so leaving it on charge for a while, then unplugging it and rebooting it often works.
I've heard it's something to do with the latest chipsets, but it sounds like a bit of a fuckup to me. But in general, if your phone goes dead, it should have left enough power to boot up again to charge, but maybe not enough to be left dead for more than a day or so - so if your battery runs out, get the phone back on charge asap.