There are also a host of textured rolling pins, mats, molds and other tools that can be used to emboss fondant to give it something other than smooth look.
That said, I rarely use fondant to cover cookies completely (I'm not a huge fan of its chewy texture), but I do like to use it (or modeling chocolate, even better!) to make small 3-D embellishments that can be easily plucked off cookies if one isn't super fond of the texture. I like all the fun things that can be made by modeling and molding it, so I definitely don't avoid it altogether. I'm in the process of shooting (on 7/2 and 7/3) a new series of videos, one of which will be about making easy embellishments with modeling chocolate. I'll be sure to share those videos then.