Not surprising
considering it is a lot easier to mis-configure and fail to update the LAMP stack than it is to secure it.
Then there are all those GUI's, themes, admin interfaces etc. that web admins install to make administration easier. What's more it is far easier to write insecure php code than it is to write secure php code.
I get several attacks a day on my LAMP server, usually they are scripted attacks looking for admin interfaces and directory traversal exploits.
My advice is install the bear minimum, use Vi and the sql command line tool to configure the stack and avoid using third party tools unless you know php and understand exactly how the code behaves and can fix any bugs or flawed validation routines. Using a simple text editor to configure a LAMP server forces one to learn how the components interact and leads to a greater understanding of the system.
I would recommend removing all the system commands that are not required to configure the server and make those that remain available to one user only (not necessarily root) and not every user of the system. I accept that this may not be possible in some deployment scenarios.


