http://en.wikipedia.org/wiki/Incest#Inbreeding
I quote :
"A study of a group of 21 made up of brother-sister or father-daughter offspring found that 12 had abnormalities with 9 of which were classed as severe."
OK, I rounded this to 50%. 12 out of 21 is more than 50%. 9 out of 21 is less. Either way, we are talking of serious consequences.
I have a developmental biology background; I performed genetic research using zebrafish and Drosophila. Two of the cornerstones of genetics are sibling crosses and back crosses (ie. breeding siblings with parents). The output from these crosses enable you to determine the inheritance patterns of given traits of interest, be they natural or genetically engineered.
I have performed more sibling and back crosses in zebrafish (a vertebrate) and Drosophila (an invertebrate) than I could possibly remember, and I can categorically tell you that it
isn’t the case that 50% of the progeny from such crosses are severely abnormal (unless, of course, they are a specific line carrying a disease allele). Somehow I think I (and the countless other developmental biologists worldwide) would have noticed if that was the case!
Of course, genetic research with model organisms utilises inbred strains where many deleterious recessive alleles have been bred out, thus increasing the chances of normal progeny from such crosses. The instances of abnormalities from inbreeding crosses of outbred lines does increase, but you don’t go from zero to ~50% when comparing progeny from inbred and outbred lines.
As for your wikipedia example, the devil is in the detail, as it is with all scientific studies. Without reading the precise methodology of the study I can’t comment on it. The simple explanation for those results is that the families chosen contain alleles for genetic disorders and are not, as such, “wildtype” matings. Indeed, the preceding sentence emphasised that abnormalities from inbreeding "...varies depending on the number and quality of inherited congenital disorders of which the family members may be carriers."