Quoting from the documentation of func StringToStringVar:

The value of each argument will not try to be separated by comma.

However with the following program:

res := make(map[string]string)
flag.StringToStringVar(&res, "foo-flag", res, "foo-flag-usage")
flag.Parse()

go run ... --foo-flag "foo=bar,baz=quux" results in res = map[baz:quux foo:bar].