One of the things I read all the time when I'm trying to work on my character design is that you have to treat your characters like tools. This is something I can understand. If you get too fond of your characters, you can't bear to kill them off, everything good and wonderful happens to them, nothing very bad ever occurs in their lives, and overall, they can end up being hollow shells of characters, as opposed to deep and believable people.
The other side of the coin is that once you've created a character, you need to get into the character's head and act out what the character would do. It's a little like role playing, for those of you who play Dungeons & Dragons. You're constantly thinking, "Okay, I'm X. How does X react to Y? What do I do?" Eventually, you learn to slip into the mindset of the character very easily. You can sympathize with him/her/it. You share their emotions, their hopes, their dreams...all because you need to get into the character's head to write consistently with your character design.
So what do you do? Do you stay emotionally detached and clinical with your characters? Or do you throw yourself into them?
I've come to realize that the trick (at least for me) is to find a middle road. I design characters who do not think or act like me. Kind of. I might throw little parts of me into them, but if I do, it's small enough that I can't mistake the character for being just like me. This huge difference between the character and me helps me regard them more objectively. I make a character profile. The profile gives me a guideline to follow for the character so that if it ever feels like I'm deviating from the true essence of the character, I can go back and look at the profile (this is something I learned to do from playing role playing games online).
As far as getting into the head of the character(s), it's often a bit tricky. One of the biggest problems I saw in role playing games was the inability to separate the "you" out of the game and the "you" in the game. This goes for any role playing game.
Writing isn't so different. Writing is just a role playing game where you play all the characters, so it's very easy to have a favorite character and easy to get the urge to make everything go well for this character, because it can become a projection of you, your thoughts, your feelings, your beliefs, etc.
This second part is the most difficult. I have to be able to get into my character's head without becoming attached to the character. To be honest, I hate killing off my characters or finding other ways to get rid of them. I don't mind throwing problems at them, because in truth, there is no story without problems for the character to solve. I do have some attachment to my characters, but this is necessary (to an extent) I think, because it tends to be a side-effect from playing the character and staying true to the character design. The trick, and I think the method is probably different for everyone (but who knows!), is to walk that fine line between attachment and detachment.