Is rc.local file to run command at boot time?
I am using this file to start various scripts and programs while the system loads. Especially mysql.server script.
Is it safe?

What operating system and version?

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Slackware 14.2

Yes, /etc/rc.d/rc.local is a place for you to add your own commands to Slackware's boot process. The script will be the last thing run before you are presented with your login prompt (runlevel 3) or starting up the graphical login (runlevel 4). Due to this, make sure all processes are daemonized (if the program supports it) or backgrounded properly (using an ampersand & at the end of the command), otherwise you won't get a login prompt.

However, I'm not familiar with a mysql.server script. Is this a personal script or something more complex? Some light googling didn't shed any light. It might be worth adding it to the rc.mysqld script, as then it can be run when the database daemon is started (and, if needed, you could add commands to stop it when the daemon is stopped or restarted).

/etc/rc.d/rc.local is for scripts that are specific to a given machine.

Of course, you can start MySQL from rc.local, but as bassmadrigal pointed out, it's better to use /etc/rc.d/rc.mysql for this.

For instance, I have used rc.local to add very specific route commands to the system configuration, or to start a few exotic process (including configuration or file backup or replication that must be run every time the computer/server starts).

BTW, you may also want to create/update /etc/rc.d/rc.local_shutdown if the command has special concerns during shutdown