There is a federal law called the Administrative Procedure Act, which requires executive agencies to follow a process while engaging in rulemaking. Part of the process is a public comment period, and agencies are required to substantively address the concerns in public comments. If, for example, the public comment process is 99% against a proposal and the agency proceeds without having a VERY good argument, it can get struck down by judicial review.

Pai knows this, and the fact that the public comments on net neutrality rulemaking were so obviously manipulated has made people think there is at least a possibility that he, or the FCC, was complicit, in order to flout the APA. The fact that the agency has gone out of its way to cover the situation up does not inspire much confidence, either.

TL;DR: A bunch of comments on a website could result in the FCC's actions being struck down in court.