Juve were awarded two contentious penalties in the match before the international break and Roma were clearly unimpressed with referee Gianluca Rocchi.
The visitors were also given a questionable spot-kick, while Roma coach Rudi Garcia was sent from the touchline and a player from each side was dismissed in the final two minutes.
Juve's victory moved Allegri's side three points clear of their rivals at the top of Serie A, and the head coach believes his side were not given enough credit for their performance.
"The decisions from Rocchi were elevated to the highest level because it was Juve-Roma," he told Corriere della Sera.
"What has been lost is the good performance of Juventus against Roma, a great team who have in [Francesco] Totti, an extraordinary player.
"Are Juventus the public enemy? There are 50 million fans, Juve have 12 [million], the rest are Milan, Inter, Roma and so on.
"Everyone is against Juve, now I realise that."
Allegri has made an impressive start to his tenure at the defending champions with seven wins from eight matches in all competitions.
Next up for Juve is a trip to bottom side Sassuolo in Serie A on Saturday.
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