The D drive is no safer than the C drive - disks fail (this applies to all computers, from home PCs to supercomputers that the likes of NASA use).
In fact, the C and D drives may not be separate drives - on a laptop, they're more likely to be 2 partitions of the same physical drive.
There are several reasons why PCs don't use the C drive for everything. One is that if there is more than one physical drive, it's much easier, (from an operating system point of view) to call the various drives C, D, E, etc. Another reason is simply tidiness and ease of administration - e.g. if all your personal stuff is on D, you could (for example) upgrade the operating system on C (XP to Vista, for example) without worrying about preserving personal data. A few years ago, it was fashionable to partition single drives into C and D - I suspect this is why you've got 2 drives.
As far as using them is concerned, use them however you like - there is no real difference.