Flags, also called switches or options, are things that you append to a command to alter it's behavior. For example,
will just list the files in whatever current directory you're in, but
# ls -l
will give you the same listing in long format. See ls for more info on that particular flag.
Note that in FreeBSD, flags are prefixed with "-" or "--" as opposed to Microsoft Windows' "/". Often a flag can be given as "--the-long-name-of-the-flag" or the much shorter and less carpal-tunnel-inducing format of just the first letter, "-t".