I love this topic which I know a few jerks I really feel sorry for:
Sylvester - I mostly feel sorry for him alot from always getting abused by that annoying little beast Tweety

which I wished he devour him in one big gulp.
Starscream - In the old classic series, Megatron never gave the poor guy respect sometimes like in the episode
Auto Berserk when Megatron abandoned him when Red Alert went haywire crazy & in T:Armada before the final battle with Unicron, Megatron never respected him until when he died which that was a sad episode & poor Alexis liked him:crying:.
Homer Simpson - Despite his troublemaking & doing dumb things, all he wants to do is be a great father & role model for his wife & kids, but I wanna punch Marge's bad sisters for always talking bad about him which I've always hated them.
Bushroot - In his origin episode, the poor guy who was a scientist wanted to make a world a better place to live & had a crush on Dr.Rhoda Dendron until when those stupid bully scientists mocked him for his plant passion which made him a supervillain but deep down he's really evil like the other supervillains.
Invader ZIM - He was hilarious & awesome, but the poor dude will never conquer the planet Earth with Dib & other adversaries getting in his way since all he wants to do is make his 2 supreme leaders proud.
Captain Gantu - He was a great cool villain which I feel sorry for the poor guy since deep down is a really lonely guy who wanted a friend(625 maybe) & when he's always yelled from Hamsterval for his failures alot which its nice when he punched his screen in that one episode and at least he turns good in the Leroy & Stitch movie.
Deadeye - In the episode
If Looks Could Kill, she was Chick P.'s old friend who was used by Dr.Wasabi who was such a jerk to crush their friendship which I feel sorry for the poor girl which Chick P. will make Dr.Wasabi pay.
Anemone - She's my favorite which I really felt sorry for her when she's being used as a pawn/tool by the jerk Colonel Dewey to become a psychotic pilot to crush Holland's crew, but she's shown great character development before turning good having to be saved by Dominique who's awesome.