Cloud had a huge number of fans (moreso than haters).
Lightning does not. Her fans are just weird and few in numbers to say the least.
Lightning is popular in Japan. :u And I don't think the hate for her is that bad here to be honest. I've only see a few very vocal haters. Most seem indifferent, or weirdly infatuated by her.
But I do remember Cloud getting hated on A LOT, along with FF VII in general. o.o People didn't like how much attention it was getting. Which is similar to the XIII situation now that I think of it... --- http://bln.gs/b/24i7sw