Yoshinori Ono has said in an interview that he actually wanted SF4 to be slightly unbalanced in order to keep things interesting, so to speak. Personally, I think it's pretty obvious that some unbalance in games is entirely intentional. And IMO you're really just deluding yourself if you don't believe that the designers themselves would intentionally make some characters stronger/weaker than others on purpose, especially when Capcom staff has specifically said so on record. Though I'm sure he isn't the only example of this.
Why would they do this?
Because people like unbalance and character variety. Just ask the MvC2 players if they would really play a perfectly balanced and toned down Marvel game. Some people like to root for the underdog character, some people want to play the gimmicky cheesebag character, and some people just want to play the strong protagonist hero or strong antagonist bastard.
But, how do bad matchups happen and what makes them bad?
Obviously, some attacks are better than others, because not all attacks are the same. But to use a very basic example, let's say character (A) has a really shitty jump arc with crappy jump attacks while the other does not -- and character (B) has outstanding anti-airs and a really good jump arc with good jump normals. What happens here is that character (A) can't rely on jumping or they will just get anti-aired, while character (B) is free to jump in all day. That's a very clear and obvious lopsided advantage/disadvantage. You can try to compensate for the weakness of not being able to jump and not being able to anti-air, but character (A) is having to deal with that weakness by playing harder while character (B) doesn't have to deal with it.
This isn't just a hypothetical/theoretical situation though, it actually does happen in games like SF3:3rd Strike where some characters really shouldn't(don't) jump in while others certainly can (and do). It isn't limited to just jump arcs though. Other things happen like a character will have a specific move like a c.MP with a good hitbox or special move that just simply shuts down the opponents options and makes the battle much more difficult. It's really easy to see why if you simply analyze why there are some 8:2 matchups in some games when the same character can have decent/fair matchups against other characters. There's usually at least one specific thing that is highly advantageous or when put into use makes the matchup highly disadvantageous.
Well, to share an amusing but fairly accurate quote from IRC:
"japan just learns their chars. america goes for that tier list
then when they lose, the tear list happens" -DS893
And it's true. Presumably for a lot of Westerners in general. I assume it's because they like to win, but I also assume it's more than just that. I'm pretty sure most people don't want to question if they were losing because their character was crap. Imagine going to an arcade and dumping quarters into a machine, losing 10 times in a row, then later realizing you just "wasted" 5$ playing a character that had little chance of winning because it was a shitty low tier character. I don't think there's many people out there that are willing to drop down an entry fee at a tournament only to pick an obviously weak character and then have to question when you lost if it was because of the character or not.
However, I'd like to say that this doesn't really reflect how I feel personally. I tend to play whichever character I feel most comfortable playing with, because I assume that I will be playing to the best of my ability if I'm able to use the characters' strengths properly. Often, the characters that I choose aren't top tier. But, to be fair, I also generally don't pick low tier characters either and tend to drop low tier characters if I find their matchups to be too horrendous.