• File::Copy's copy puts a lot effort in being portable.
• It's well tested.
• It doesn't launch a seperate process, so it's faster and uses less memory. Instead, it uses a system call (or Perl code if the OS doesn't have such a call).
• It can copy from/to file handles instead of just from/to files.
• Its arguments are not subject to shell interpretation. (The way in which you used system is buggy and unsafe.)
• It's makes checking for success much easier.
• It provides meaningful error messages in $!, on most systems.

On the other hand,

• Your expression is not portable.
• It's not well tested. In fact, there are bugs.
• It launchs *two* seperate processes, so it's slower and uses more memory.
• It can't copy from/to file handles, just from/to files.
• Its arguments are subject to shell interpretation (although that can be fixed). The way in which you used system is buggy and unsafe. (Bug 1)
• It thinks it succeeds even if the copy fails, as long as the shell was successfully loaded. (I think.) (Bug 2)
• $! does not contain what you think it does here. It definitely does not contain why the copy failed when it does. (Bug 3)