Good question. I personally love cufflinks; I typically wear them with suits, but during the school year, I really do not have that option, so I go to wearing them casually such as now. In fact today I am wearing a Burberry french cuffed shirt, untucked, with jeans and navy blue silk knots. I love the look. Personally, I think it is better that most people don't wear them, as it makes those that do wear them, stand out a little more. Certainly I wouldn't want to be accused of following some fad. I would think that the onset of french cuffed shirts from cheaper retailers like Banana Republic would bring more people to wear them, however I have really not seen any students on my college campus wearing, them, except me of course.
If you like them like I do, wear them proudly.