This is a question I get asked a lot.
Rather, I also get heckled for it. Even by people I hire.
For me, it kinda goes back to using a calculator in math class.
A lot of DBAs, developers rely on tools to get the job done, and that is fine.
But what if you were in an environment where those tools were not allowed? What if you were in an environment that was foreign to you, and you needed to help fix a problem straight away?
What if there was no google? Oh noes.
Tools are great, they make our lives easier. But don't you want to know how MySQL is doing something, or why?
Friday was a perfect example. One of our internal clients has circular replication setup between two machines. One of the machines ran out of disks pace (Bad Shinken for not finding that in time.) The VIP was setup to be a smart active-active VIP so after the fact we had one machine in the middle of some updates, and we had another machine that crashed, got fixed, started taking updates again, crashed, and had to be fixed.
You may be able to find a tool on the web that claims I can fix your data in 10 seconds or less. Unless you have read it's source code, and it is extremely important data, do you want to trust that tool to it?
What if you knew how to use mysqlbinlog yourself export out the updates from both machines as best you can, give it a proper known start and stop point on each machine, a known state that you trust because you know what you are doing, apply the updates through the mysql cli, reset replication to the last exported and execution log position, and voila.
How do you figure out the start position for the mysqlbinlog export? By looking at the last executed log position from mysql's show slave status of course. :-)
The tool may have worked, but you took it on faith. If you know how to do it with the tools MySQL gives you natively, there is nothing to take on faith. You
see it work right then. More importantly doing it this way you can see when something fails or goes sideways during the repair (if it does) and you can react better to it, because you see the failure. You don't have to troubleshoot where the failure occurred. You see it happen, you know exactly what line.
For me, bottom line, it is great to use tools. It is also great to know how to do it with what MySQL or Linux gives you out of the box.