from http://www.word-detective.com/100297.html:

Mud on the superhighway.

Dear Word Detective: I've searched the entire World Wide Web looking for the origin of the
phrase "Your name will be mud." I think it might have come from the name of the doctor who
treated John Wilkes Booth (Dr. Mudd, I presume). -- Jerry McFadyen, via the Internet.

Searched the whole web, eh? Well, by now I'm sure that you've come to the same conclusion
that I reached a while back, namely that if you're looking for solid, useful information on the
Internet, you're barking up the wrong medium. There are exceptions, to be sure, but in
general trying to do serious research on the web is akin to asking a housecat for help with
your homework. Someone needs to explain this to Al Gore.

Thank heavens for books, therefore, especially ones such as "Devious Derivations," written
by Hugh Rawson and published by Crown. Mr Rawson devotes an entire page in his book to
the theory you have evidently heard: that the phrase "Your name will be mud" is connected
somehow to the Dr. Samuel A. Mudd who treated President Abraham Lincoln's assassin,
John Wilkes Booth. Doctor Mudd may or may not have been in on the 1865 assassination
conspiracy with Booth, who had broken his leg escaping from the scene of his crime. In any
case, Mudd was convicted of conspiracy in the trial that followed, and his name, to the
general public, certainly became "mud" in the sense of the phrase -- despised and reviled.

But Doctor Mudd's name is certainly no more than an interesting coincidence, for it cannot
have been the source of the phrase. "Mud" had already been in use for more than 200 years,
since at least 1708, as a slang term for a fool. According to Christine Ammer, in her book
"Have A Nice Day -- No Problem!" (a very fine dictionary of cliches published by Plume),
"mud" was commonly applied in the 19th century British Parliament to any member who lost
an election or otherwise disgraced himself.

The Phrase Finder also validates this:
http://phrases.shu.ac.uk/meanings/424000.html