First, stepper motors do get pretty darn hot. A common "safe" temperature I see thrown around is 80C, but I'd try to keep it well below that.
Since you're not feeling any difference in resistance when moving the head around and print quality isn't effected then perhaps the current is simply set too high for that motor. You can tweak the motor current on the driver board underneath the machine. You can find instructions for that on the page linked below. But please, be careful, and read everything before trying to adjust anything.
http://wiki.ultimaker.com/Electronics_build_guide
Alternatively you could mount a heat sink on it to help it cool off.
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Dim3nsioneer 557
Obviously the y stepper driver is set to a higher current compared to the x stepper driver.
You may reduce the current. Please check the http://wiki.ultimaker.com/Electronics_build_guide. Especially make sure, you don't turn the potmeter on the driver pcb into the wrong direction; you could destroy the driver with a too high current. And don't run the UM1 electronics longer than 30s without the cooling fan.
Although I switched my UM1 to direct drive some time ago (and therefore have reduced mechanical resistance in the axes), I think it should be possible to run the motors with the standard setup (i.e. including the short belts) with a current that still allows you to touch the motor.
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