New Kitten and Grumpy Cat...

One if my roommates just brought home a new kitten about 2 days ago. We think he is about 6 weeks old; he is very little and very uncoordinated and naps about every hour.
My other roommate and myself each have a cat. Buffalo (my roommate's cat) is about 3 years old and male. Monkey (my cat) just turned 2 last month and is female. We expected that the new kitten would not be liked right away by Buff and Monkey. Buff hated monkey when they first met 2 years ago, but they are now somewhat friends and play and hang out together. 
The new kitten (Momo) scares Monkey... Her behavior around Momo confuses us all. When she sees him she growls and hisses (like we expect) but when he moves or looks at her, she will cower and run into my room and hide. She has been around many Dogs and has not acted like this at all...  
We have been keeping Momo out of my room, so that stays her safe zone, but we just do not understand how she can be scared of such a tiny little fuzz ball. 

Can I get some advice on how we can help her get used to him or at least not be afraid of him? 
We will not all be living together for much longer, but I would like to get a second cat for myself some day in the future and would like any information on how to make this transition easier for her.

Anything helps, the new kitten has been so much fun, we would all love it if all of our cats could get along and play together... 

Monkey's reaction is quite common. You are right about hissing and growling being the usual ways of meeting newcomers but avoiding them is also another. It's been only a couple of days. In time, Monkey will be very curious about the little one. Maybe she is a bit confused about what a kitten is. 

In the meantime read this http://www.thecatsite.com/a/introducing-cats-to-cats  to help you. 

That may be the case.. The only other cats she has met is Buff, and the few neighbor cast she has met back at my mom's place, and my moms little dogs (that she likes to stalk/hunt)... I just find it so strange for my very confident cat to be so hesitant around something that is 5 times smaller than her.
I will check out the link you shared. 
Thank you

If the kitten is very uncoordinated, then Monkey's reaction could be partly because she can't understand his body language. If she can't read what kitten's saying then is natural that she'd be very wary.

I used to know a 3 legged dog. My lab couldn't stand him, and we're pretty sure it's because he moved differently and she couldn't 'read' him so well.

That article link is a good one. These are useful too:-

http://www.thecatsite.com/a/the-ultimate-yet-simplified-guide-to-introducing-cats

http://www.thecatsite.com/a/the-multi-cat-household