Different people just use Facebook differently. Some people just don't see it as a mirror image of their friendships in real life. Some people will be friends with people in real life without having them as their online friend on Facebook and vice versa. When I used to have Facebook, I didn't have any family members or distant family members as Facebook friends at all. Not my sister, my cousins, aunts, uncles, boyfriends sister, his parents etc... Even though I liked them, I wanted to be free from them knowing even the slightest thing about my life such as what my plans were, what my friends were like, racey/sexy/expletive or innuendo-heavy wall posts/status updates/photos etc.. I even rejected or deleted some of my best friends and even my own boyfriend as Facebook friends because they were a right pain on Facebook.
Basically, some people will just see Facebook for what it is, Facebook. To them it won't be a mirror or extension of their friendships in real life. A lot of people I know, only have extremely close friends on Facebook. You'd be their friend in real life but to socialise with online, they'd just like really really close friends.
Also, don't forget, Facebook has two primary purposes 1)To socialise and interact and 2) To share/put info about you on there.
A lot of people might be happy to interact and socialise with online with a whole range of different levels of friendships -from their best friend to coworkers, to someone they've only met twice. But for the other Facebook reason - to share things about themselves or the fact that people would be able to see posts,photos, likes, statuses etc.., they might have a stricter friend filter.
Not everyone who is happy to interact with all is happy to share with all. Someone might be happy to have you on Skype or MSN messenger as a friend but not as a Facebook friend. Not because they don't want to interact with you as a friend, but maybe because of the "one can see/find out anything about you" aspect of the Facebook profile, they'd prefer to only restrict that privilege to a select few. Of course there are settings to control this but people don't have to use them. They can reject people instead. Not reject them as a friend in the true sense of the word - but merely reject them as a Facebook friend only.