I've been trying different covers lately and they all have what seems like disgusting lube/spermicide and a rubbery smell (and I'm guessing taste).  Wouldn't a clean, uncovered member be preferable to that other mess?

Strictly speaking, there's a chance you can catch an STD from a uncovered dong in your mouth. The odds aren't very high for anything but HSV, which is only moderately high. Basically, they would need to have an  outbreak, or be just prior to an outbreak to catch it, and even then the worst you'd get is a coldsore, which most people have anyway.

 
I'm also betting that the cover provides some protection from teeth, and is easier to get down than an uncovered dong. I've never blown a dude, so, this is just extrapolation on my part that seems to hold water.  

 
So, the science doesn't really hold up, but lets look at it another way. There's an emotional thing going on here being that we're dealing with humans, not robots. The reason i'd bet most do it is because they *feel* safer, even if it's not a conscious thought, and that's reason enough really.

...not that they like it, but they've gotten used to it.  They prefer to have that feeling of safety and they've experimented with enough condoms to find the one that has the least offensive taste and smell.

... another reason some women prefer CBJs is they can't stand CIM.  Unless a provider is sure the guy won't do that, using a cover lets her not have to worry about it.  Any bad taste of the cover is outweighed by her strong dislike for cum in her mouth.  

I will definitely never see a provider who's TER profile states CBJ. Even though I am not huge BJ guy and CIM is not important to me, I do enjoy the feeling and the visual but rarely have I found a lady that can finish me that way without some hand stimulation.  
If she wants to Cover it to suck it, she will probably not be a very passionate kisser as well. Maybe wrong on that but just my gut impression.

On top of that , i am a female condom only guy for FS.

We are all entitled to make our own choices!!!!

... there's no correlation between kissing passion and giving CBJs.  The best kisser I know does CBJs in p4p (the CIM thing).  

Some ladies will suck a bare dick but not kiss on the lips.  Go figure!