One of the things my dad likes to kid me about is how mean I am to my characters. I have no problem throwing rock after rock at them. After all, aren't the great stories all about conflict?
Think about it. If there was no Mr. D'Arcy, there would be no Pride and Prejudice. If Scarlet and Rhett met, fell in love and lived happily ever after there would be no Gone with the Wind. It's opposition to your main characters that creates compelling fiction.
I've heard it said that story = conflict. I think that's true. Not that conflict has to always be in the form of another character. Sometimes the conflict comes from inside your character. Or maybe it's Mother Nature (think Twister).
When you're writing fiction, this is not the time to be nice to your characters. This is when you get the chance to let it all out. Slap 'em around! LOL It's because our fictional people become so real to us that it's hard sometimes for writers to throw their "babies" into the fire. But we must. We really must.
What is conflict exactly? It can be as small as a husband and wife disagreeing over where to go for dinner (well, maybe that's not small ...), or a duel between two warring knights. Throw two people of opposing beliefs in the same room together, and you're bound to have an interesting scene.
Those are the sort of opportunities we should look for in our fiction. Purposely put your protagonist into situations that make her/him uncomfortable, that stretch them. Don't go easy on them. These aren't real people, it's okay to be mean.
When was the last time you read a novel or watched a movie where the lead walked into a room and ran into her worst enemy? I bet you were waiting on the edge of your seat to see what would happen. Come on, admit it. You wanted to read/watch them fight! If they'd pulled each other into a hug and everything was hunky dory, that would've made for boring fiction. They can make up at the end of your story. But in the middle we have to remember to think of worst case scenarios for our characters. And then make them worse!
Someone once described the structure of fiction as getting your protagonist up a tree, throwing rocks at him, then getting him down. So ... what rocks are you going to throw at your character today?