I don't think this is a general Linux problem. I had this under Windows XP too. 
It has something to do with the Advanced power management which seems to be set 
to 128 per default from the hard disk producer which lets the hard disk sleep 
after a short time. At least under Linux it is very easy with one line in 
/etc/rc.local to set the value to 255.
hdparm -B255 /dev/sda
I don't see the problem and it doesn't seem to kill the hard disk so fast 
otherwise much more people had huge problems and the producers wouldn't ship 
them with activated advanced power management.

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High frequency of load/unload cycles on some hard disks may shorten lifetime
https://bugs.launchpad.net/bugs/59695
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