That won't just exclude HTML entities from being matched, it will exclude any & character that is in the same line as a semicolon somewhere to the right of it, because .+? also matches whitespace.

Instead, you should match for HTML/XML entities specifically. There are three forms that they can take, and the corresponding regexes for matching them would be:

  /&#[0-9]+;/ - character referenced by decimal number

  /&#x[0-9a-f]+;/i - character referenced by hexadecimal number

  /&[a-z]+;/i - character referenced by name

Putting it together, you get this regex for matching an HTML entity:
  /&(?:#(?:[0-9]+|x[0-9a-f]+)|[a-z]+);/i

Although that's kinda messy and pedantic, and you can probably get away with using this simplified version:
  /&#?[0-9a-z]+;/i
(Unlike the more pedantic version, it would match some false positives such as &#amp; or &1a2b3c;, but what are the chances such constructs will appear in the input document?)

To do what the OP requested, wrap everything after the & in a negative look-ahead bracket like choroba suggested:

#                  10        20        30        40        50
#          ---------'---------'---------'---------'---------'----
my $str = "& ... & ... & ... &no_entity; ... & ... ;";

while ($str =~ /&(?!#?[0-9a-z]+;)/gi) {
  print "Found ampersand at position ".pos($str)."\n";
}
[download]

Output:

Found ampersand at position 32
Found ampersand at position 48
[download]

(i.e. it only matches the last two & characters in $str)