Don't shoot the ref
Of course the goal should have been allowed. However, in my experience as a spectator of team sports and basketball player, I've never seen or played in a match where a team has dominated and deserved victory, only to have the referee steal it from them. England made exactly the same mistake they made against France and the same mistake several teams have made throughout this competition: scoring a goal, then waiting for the match to end. Portugal was offensively impotent for so long and not particulary solid at the back, had England continued to apply pressure, they surely would have scored one or two more, with or without Rooney.
Still, as a more-or-less neutral observer, the second half was quite snooze-inducing until Portugal scored.