With less than a $10 price difference, you can't go wrong with either the Trek FX 7.3 WSD or the Cannondale Quick 4 Fem. You can always swap out tires for more or less tread. And a carbon fork might shave off a few ounces and soak up a little more road vibration, but unless you plan on riding more than 20 miles at a time, I'm not sure how much of a difference you'll notice. (It's interesting to note, however, that the Cannondale does offer this bike in a $2,029 fully carbon frame.)
As for components and other differentiating bells and whistles, it looks like both bikes offer quality, come with a women-specific seat, and have braze-on eyelets to mount racks, panniers, and fenders, an important element if you're going to use the bike for commuting.
So really, it all comes down to fit: The Trek FX 7.3 WSD ($640; trekbikes.com) has four women's specific design diamond and two step-through frames, while the Cannondale Quick Feminine 4 ($649; cannondale.com) comes in five sizes, from small to jumbo. On any kind of ride--whether it's commuting to work or riding on a gravel country road for pleasure--you're going to want to love the way the bike feels. Both of these options offer upright riding geometry, which is generally comfortable, but I recommend trying to spend some quality time in the saddle of each bike before you buy to determine which one you'll like to ride best.