How do you tell git to permanently ignore changes in a file?

git based approach: use a production branch and keep the changes specific to your production environment in there. To release to production, merge your master branch into your production branch.

deployment based approach: use a tool (such as capistrano/cfengine/...) to automate your deployment process. This has many advantages, one of them is the ability to keep configuration separate from your code.

You could use a smudge/clean process (a gitattribute filter driver, described in ProGit)

Each time you update your working directory, you would have the opportunity to replace the content of your .htaccess with a predefined one, correct for your current environment.
In the clean stage, you would then restore the original content, as if you had never touched that file.

Simply tell git to assume the file is unchanged:

$ git update-index --assume-unchanged FILE [FILE ...]

From the manual:

   --assume-unchanged, --no-assume-unchanged
       When these flags are specified, the object names recorded for the paths are not updated. Instead, these options set and unset the "assume unchanged" bit for the paths. When the "assume unchanged" bit is on, git stops checking the
       working tree files for possible modifications, so you need to manually unset the bit to tell git when you change the working tree file. This is sometimes helpful when working with a big project on a filesystem that has very slow
       lstat(2) system call (e.g. cifs).

       This option can be also used as a coarse file-level mechanism to ignore uncommitted changes in tracked files (akin to what .gitignore does for untracked files). Git will fail (gracefully) in case it needs to modify this file in the
       index e.g. when merging in a commit; thus, in case the assumed-untracked file is changed upstream, you will need to handle the situation manually.

Found in How to Ignore Changes in Tracked Files With Git