Most Harry/Hermione shippers have only seen the movies, in which Ron is a complete and utter idiot (which is not true) and Harry is God and the most sensitive guy on Earth (which is also not true). If they believe that, just wait until the fifth movie comes out. If the directors do it right, their precious Harry will start to scare them then.
For those that have read the books, the reason they ship Harry/Hermione is either:
A. Because Ron is a "mindless, poor, insensitive pig". Which is not true. He can be lazy, but he's not down right retarded. He cares for Hermione, and it is displayed in the books innumerable times. And who cares if he's poor? If Hermione is the all merciful, perfect goddess that most of you all seem to believe, she couldn't care less about Ron's financial status. OR
B. Many people, including my family, believe that the hero (aka Harry) should get the girl (aka Hermione). Well, if this were to happen, Hermione would have been pushed aside, being downgraded to damsel in distress. I don't think Hermione fans will be too happy about that. J.K. knew this ahead of time, so she paired Harry with Ginny (which was honestly the most random pairing I have ever seen; I saw Ron/Hermione coming ever since book 1). OR, possibly even
C. Ron and Hermione fight a lot. Well, what couple doesn't? There is something there between the two. Passion, emotion, whatever you want to call it. Harry and Hermione hardly fight. Or embarrass or effect each other (other than Hermione's mothering, of course). They are simply good friends.
Now, if you ship Harry/Hermione, while still liking Ron and not falling into the categories I just mentioned, I salute you and respect your opinion. I've just seen so many Harry/Hermione shippers with such petty reasons, and it is rather annoying. Otherwise, though, I am fine with it.