Rather than getting bogged down with alternating between the start and end strings and then doing a repeat substitution, just capture the middle bit and tag a '?' on either end. This works with the sample string you provided:

$ perl -Mstrict -Mwarnings -E '
    my $string = "---------xxxxxxxxxxxxxxx------yyyyyyyyyyyyyy--------
+";
    $string =~ s/^-*(.*?)-*$/?$1?/;
    say $string;
'
?xxxxxxxxxxxxxxx------yyyyyyyyyyyyyy?
[download]

Update: Actually, that may not be what you want at all!

I read:

• "replace all characters ..." [plural] "... with another character" [singular]
• "The output is: ?xxxxxxxxxxxxxxx------yyyyyyyyyyyyyy?" [wanted output]
• "replace ever - ..." [plural] "... with an ?" [singular]

So, assuming I've completely misinterpreted your question, I'd recommend ++rjt's solution. However, if you still wanted something without alternations or repeating, you could use this:

$ perl -Mstrict -Mwarnings -E '
    my $string = "---------xxxxxxxxxxxxxxx------yyyyyyyyyyyyyy--------
+";
    $string =~ s/^(-*)(.*?)(-*)$/"?" x length($1) . $2 . "?" x length(
+$3)/e;
    say $string;
'
?????????xxxxxxxxxxxxxxx------yyyyyyyyyyyyyy????????
[download]

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