That apology cost nothing. If the same circumstances happened again, Israel would kill some more Turks.
In the meantime with Gaza still closed as a port and no one trying to get in the apology works well.
There was an attempt last year by another Gaza-bound flotilla, but this time the Turks didn’t allow it to even leave the dock.
Very likely, they didn’t wish to inflame matters further on their part.
Like you said, an apology costs nothing. It might help patch things over between Turkey and Israel as well. And it sends a message to the Iranians, with whom the Turks are growing increasingly wary of.