ignoring files/directories in git

I'm working on a project by myself and using git mostly just to learn about
it.
In my project I have several directories I do not want to have git ignore.
One of them being
cache/ and the other log/
I've added them to the .gitignore file which I have in the initial directory
of the repository
The contents of my gitignore are:

.settings
.cache
cache/
log/
.project

However, if I do 
git add .
It will add the files from cache and log anyways.
I know git add . will add anything that hasn't been added but shouldn't it
ignore files in .gitignore?
If not, what is the point, I would just ignore them manually anyways. 
The main reason i like doing git add .
is because i'm using symfony php framework which makes good use of scripts
which generates lots if initial files for you and thus adding one at a time
would be a pain.

Any idea what might be going on here?  I thought maybe I had added those
directories before putting them in .gitignore so i used git rm -r to remove
them but they still show back up with doing git add .

Thanks in advance
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