Search engines do not index php pages which look like
http://domain/somefile.php?somefunction=function&id=id

Actually, yes they will.
It may not perform as well in the SERPs as it might with keywords in the URL, but they will index it just fine.

Indeed, Google recently wrote a blog entry saying it was just fine to leave these urls as is.
http://googlewebmastercentral.blogspot.com/2008/09/dynamic-urls-vs-static-urls.html

Is it necessary to create rewrite rules for all php files so that they look like directories?

http://domain/file.php --> http://domain/file

... or is it not necessary and search engines will index the content of php files if they end with .php (without any "?id=..")?

No, they are quite happy to index .php files

[edited by: caveman at 4:50 pm (utc) on Dec. 2, 2008]
[edit reason] Delinked links [/edit]