The reason I was given is twofold. 1) If your RAID card dies it's nice to be able to plug drives into any controller and be able to access the data. 2) "look at how often MDADM fix bugs. Now look at how often your RAID card firmware gets fixed... use MDADM".
Modern filesystems like btrfs & zfs both prefer to deal with the RAID aspects themselves as it gives them far more control. Even if you're a hardware raid afficianado, I wouldn't recommend formatting (eg) ZFS on top of a hardware raid pool.