There are two types of third party protest voters and they get conflated a lot even though the philosophies and rationale for it was totally different.
1. The accelerationists would be the ones who said there wasn't enough difference between Trump and Clinton to warrant giving away a vote. This tended to be followed by the idea that the Dems would get the message and move left or that things would get so bad that more radical changes would become more viable. I tend to apply this logic to the Jimmy Dore wing of progressivism. They encouraged protest votes wherever you were. (See Sam Seder's debate with Jimmy Dore)
2. The "safe state" protest voters. In states where Clinton was going to win (I'm from NJ/NY) regardless, you could vote third party to register your dissatisfaction and attempt to get a third party to 5% of the vote aka the FEC funding threshold. Basically, you cast a vote that is harmless and could have an upside of adding a third party into a firmer footing to push policies that aren't available otherwise. Briahna Joy Gray was in this camp. She had this whole other thing about trying to get disaffected voters out in these blue states so that they could vote down ballot but I'm really not sure how much merit there is to that bit. The important thing is her approach was still to vote Clinton anywhere it's close; just that you don't have to in safe blue states. (She explained this on a podcast that I could pull up if anyone is actually interested though this summary mostly covers it imo).
The ones that fell into category 2 just don't seem harmful to me.