...though I know that one of the two companies is on the webpage

Look at this line:

@companies = ("FOO,BAR");
[download]

You are setting companies to an array with one element, the string "FOO, BAR". You want to set it to two elements in one of the following ways:

@companies = ("FOO", "BAR");
# or
@companies = qw(FOO BAR);
[download]

better yet, you could set your regular expression to match either one and ditch the for loop:

# Use quotemeta if companies are not really
# foo and bar and contain metacharacters.
my $companies = join("|", map(quotemeta, qw(FOO BAR)));
print "$1\n" if $content =~ /($companies)/;
[download]