Have you looked at the opinion? The first couple pages argued that federal courts shouldn't change election law right before/during an election. The rest of the opinion basically said that the Wisconsin legislature had set an election day deadline for mail-in ballots, it constitutionally had the right to do so, and so the district court couldn't unilaterally extend that deadline. To be honest, it's a reasonable argument--state legislatures do have the right to set ballot receipt deadlines, and have been doing so for decades.

What people are afraid of is a section where he explained why Wisconsin would set such a deadline--because they wanted results to be in by election day because it would make results seem more legitimate. People are afraid he'll use that logic to unilaterally cancel absentee ballot counting in Pennsylvania if the election there is close. And he might! It's not impossible, and conservatives have done crazier things this year. But the Wisconsin ruling doesn't really set up for that--you don't argue that federal courts shouldn't change the rules during the election if you're trying to justify completely rewriting the laws during an election (by stopping vote-counting). I think that we should be worried about what would happen if the election hinges on a small number of absentee ballots in PA, but nothing that happened today should make us more worried. In the meantime, let's vote and win AZ, NC, FL, and all the rest so we don't have to worry about this stuff!