Noone cand read the file except for those who have access to the file. You must make the code readable (but not writable) by the web server. If the php code handler is running properly you can't read it by requesting by name from the web server.
If someone compromises your server you are at risk. Ensure that the web server can only write to locations it absolutely needs to. There are a few locations under /var which should be properly configured by your distribution. They should not be accessible over the web. /var/www should not be writable, but may contain subdirectories written to by the web server for dynamic content. Code handlers should be disabled for these.
Ensure you don't do anything in your php code which can lead to code injection. The other risk is directory traversal using paths containing .. or begining with /. Apache should already be patched to prevent this when it is handling paths. However, when it runs code, including php, it does not control the paths. Avoid anything that allows the web client to pass a file path.