Most med schools say that they do not discriminate on the grounds of disability unless your disability would prevent you from fulfilling your duties as a doctor as stated in "Good Medical Practice" by the GMC.
I'm not sure how bad chronic fatigue is or how much it affects you personally, but it'd definitely be worth phoning any med school before applying to check that it won't affect your application.
On the other hand tho, being a doctor can be very tiring/exhausting for people who are healthy. So I guess you have to think about whether you could cope with it given you've got CFS...