Why do many pharmaceuticals contain fluorine?
A definitive reference is:
"The Many Roles for Fluorine in Medicinal Chemistry" J. Med. Chem., 2008, 51 (15), 4359–4369.
In reference to the bullet points:


Fluorine obviously affects $\ce{p}{K_{a}}$ and can make an acid stronger but also a base weaker which could be advantageous when optimising a drug candidate (lead) molecule.  
I guess here they refer to $\ce{-CF_3}$ which can increase lipophilicity  
That's one of the most useful roles of fluorine. A lot of times you may have a very potent and selective molecule, but when you test it in vivo let's say in rats, it has no effect because it gets metabolised i.e. chemically modified to an inactive molecule by the rats liver (and other mechanisms). This can maybe prevented by changing to an $\ce{C-F}$ bond. For example electron rich aromatic sites are prone to metabolic oxidation. You can block this by fluorination of this site, exchanging the proton for a fluorine.


Have a look at the paper on top, you will find a new world of information.