What do the percent signs in SystemRoot represent?

Substituting environment variable values

To enable the substitution of variable values at the command line or in scripts, enclose the variable name in percent signs (that is, %variablename%). By using percent signs, you ensure that Cmd.exe references the variable values instead of making a literal comparison. After you define variable values for a variable name, enclose the variable name in percent signs. Cmd.exe searches for all instances of the variable name and replaces it with the defined variable value. For example, if you create a script that contains different values (for example, user names) and you want to define the USERNAME environment variable for each user with these values, you can write one script using the variable USERNAME enclosed in percent signs. When you run this script, Cmd.exe replaces %USERNAME% with the variable values, which eliminates the need to perform this task manually for each user. Variable substitution is not recursive. Cmd.exe checks variables once. For more information about variable substitution, see For and Call

From the above Technet description, the % signs are used to ensure that "cmd.exe" does not literally use the term "systemroot" and references the systemroot variable correctly (So therefore %systemroot% is recognised correctly as the C:\ drive, if C:\ is your systemroot).