Advantages of having separate transport and DAC:
The transport (or CD player) has mechanical parts to wear out (the tolerances needed to play CD/DVD are very small), but stupidly the drawers seem to break as often as anything else. Separating out the DAC allows a smaller investment in that half of the source. Note that I'm referring to the hard drive where a computer is used, even though computer/audio interface products are called transports.
Going separate can allow for a relatively inexpensive upgrade path if you already have a CD player.
Going separate plays into the hobby aspect of audio as it gives you an couple of extra ways to swap/mix/match equipment. It also looks cooler to have more equipment.
Digital source is the newest and so fastest changing technology in audio. Going with separates reduces the financial investment in either transport or DAC technologies. For instance once you go with separates you can jump from spinning CDs to ripping them (using your computer).
Top drawer CD players are very expensive (several times the cost of comparable separates). The price where separates equal the sound quality of CD players keeps dropping. In fact it could be argued that any "audiophile grade" CD player can be bested by separates at the same price (starting currently at say $300).
Some audiophiles (including well respected ones) feel that almost any decent/modern transport or CD player does not introduce significant distortions, so they recommend investing more in the DAC. CD players typically invest proportionally more into the transport.
With separates you can introduce digital room equalization in the digital realm (which should be more ideal than after the signal has been converted into analog.
Since small digital signals are very suspectible to "dirty" A/C power, it's easy to use batteries for a low powered DAC if that's a problem where you live.
It generates more business for digital and power cable manufacturers.
