He's just a troll is a silencing tactic and excuse for sexist incidents in which the perpetrator is explained as a troll, that is, someone who doesn't really hold sexist viewpoints but expresses them in order to annoy people, upset people, or play and experiment with social norms.
There are several problems with this:
Emphasis on intent. The idea that identical behaviour should be viewed differently when it's "trolling" rather than "what he really believes" means that the intent of the behaviour, rather than its effect, is viewed as the meaningful way to evaluate it. But the effect is often identical. Trolling can make women and others feel just as unsafe in geek communities (if not more so, since trolling often uses extreme rhetoric or positions) as genuinely meant threats. This emphasis on intent privileges the person doing harm, rather than the target.
It's still intended to harm women in any case. A troll may not believe himself when he says that, eg, women are provably less intelligent, but often the claim is intended to upset or undermine a particular woman.
Disinguenous claims. Not all claims to be "just trolling" or "just having fun" or "playing with mainstream norms" etc are genuine, nor is it easy to tell, which means that targets have to weigh up the risk that they're dealing with genuine threats.
Playing into existing power structures. Even genuine trolls who express sexist and other discriminatory sentiments are using societal power to amuse themselves at the expense of disempowered people.
Trolls often view (and publicise) any attention they receive in response as "winning" the game they are playing. Unless a target wishes both the troll and a lot of onlookers to regard her as the "loser" and him the "winner", she needs to be silent about even noticing the trolling, let alone acknowledging the effect on her, which leads to the usual problems of silencing: feeling alone, feeling disempowered, making sexist voices in geek culture much louder than opposing voices.