I think it has something to do with our personalities and our historical comparison to flowers. As women, we embody or attempt to embody a lot of the traits that people find attractive about flowers - beauty, delicacy, softness, smells, and even (in some cases) longevity/hardiness or fragility. Our historical gender roles even dictated such traits for us, and historical sources have long compared women to flowers.
For example, I love carnations. Favorite flower, hands down. I love them because, of all the flowers, they come in so many colorful varieties. They smell wonderful, a soft and sweet fragrance that reminds me of how the air smells after rainstorms or the perfumes I love to wear. They also last a long time (given proper care) - much longer than any other flowers I've encountered. For me, roses don't do it - they wilt too quickly and they're overdone in terms of gift-giving. Carnations are more what I hope for - beauty, a touch of fragility, with resilience and variety: a lot like my personality.
When my fiancee brings home carnations, I know he's been thinking specifically of me because he knows they are my favorite. So, rather than grabbing the nicest-looking bunch of flowers and hoping, he deliberately seeks out colors he hasn't gotten me before or mixes colors together to form his own bouquets of carnations. When I see them, it reminds me that he knows me, loves me, and dedicates time in his life for me.
So, women like the flowers that best match their own personalities or embody traits that they want to emulate. Some are hopeless romantics - hence, roses. Some prefer hardier varieties, like my passion for carnations. Others prefer the exotic, or the strange, or even the dead (I had a friend who had a penchant for half-dead roses in coffins). I don't think it's true of all women, but the subconscious element of preferring flowers that embody traits we prefer - or carry historical messages (i.e., certain colors and flowers have long-associated meanings to them) is certainly there, and it's probably underlying our desire to simply have pretty things that remind us of people we care about.