I think it depends on the joke and how well researched it is. I remember when David Baddiel was a TV critic on the Mercury Awards the year Norma Waterson nearly won it. After she'd performed, all of the critics had their say. Baddiel made a comment along the lines of "the problem that I have with folk music is that it all sounds like the theme to Captain Pugwash". This annoyed me because of the sheer ignorance behind it, never mind the factual inaccuracy.

However, if the comedian has done some level of research into folk music, or if they are laughing with us rather than laughing at us (as various comedians such as Billy Connolly, the Fast Show team, Reeves and Mortimer and a good few others have done over the years), then it is to be encouraged and enjoyed. The ability to laugh at yourself is a commendably British trait.

Going back to the original points, folk music has probably never been cooler. Regardless of your opinions on the likes of Eliza, Mumford and Sons, Kate Rusby, the Unthanks, etc... what they have undeniably done is destroy the myth that folk music is the sole preserve of Aran sweater-wearing, tankard-swinging beard wearers. Any comedian trotting out that old cliché today would just look a bit foolish.