How to exclude file only from root folder in Git

Use /config.php.

Older versions of git require you first define an ignore pattern and immediately (on the next line) define the exclusion. [tested on version 1.9.3 (Apple Git-50)]

/config.php
!/*/config.php

Later versions only require the following [tested on version 2.2.1]

/config.php

From the documentation:

If the pattern does not contain a slash /, git treats it as a shell glob pattern and checks for a match against the pathname relative to the location of the .gitignore file (relative to the toplevel of the work tree if not from a .gitignore file).

A leading slash matches the beginning of the pathname. For example, "/*.c" matches "cat-file.c" but not "mozilla-sha1/sha1.c".

So you should add the following line to your root .gitignore:

/config.php