He's a nice guy even though he looks kind of scary which is a disadvantage for him.
He looks like a tough guy, but he's actually quite nice. His looks work against him.
この場合、次のように言うと自然な感じで良いと思います。
ーHe's a nice guy even though he looks kind of scary which is a disadvantage for him.
「彼はちょっと怖そうに見えるけど優しいから、損をしている」
ここでは、disadvantage を使って「損」を表現すると良いでしょう。
ーHe looks like a tough guy, but he's actually quite nice. His looks work against him.
「彼は屈強な男性に見えるけど本当はとても優しいです。[見た目](https://eikaiwa.dmm.com/uknow/questions/11841/)で損をしている」
to work against「不利に働く」を使って「損」を表現することもできます。
ご参考まで!