It's much more likely that your child will have a bad reaction to the vaccine than to actually get the disease.
What bad reaction? What likelyhood? Which vaccine? Don't assume this dichotomy because as far as I'm aware, in 99% of the cases it simply doesn't exist. What little side effects there are are nothing you would concern yourself with, certainly not compared the consequences of getting the disease in question.
from their individual viewpoint, there's a higher risk from the vaccination than there is from the disease
A viewpoint established by misinformation and mass hysteria. That's not meant as an insult - these people are being misled by pernicious echo chamber of plausible sounding myths.
if you don't like the deal just don't go there.
Which is obviously much more beneficial for them, because that way they get less ad impressions and less word of mouth.
These sites give you content in exange for ads
No they don't, they give advertisers potential sales in exchange for money. You are the product being sold to advertisers. There is no burden of responsibility on the user's part to purchase anything from the advertisers, or to look at the ads. It's the burden of responsibility of the site to give you a compelling reason to be their product. Bombarding the user with easily circumvented malware riddled spam every time they try to use their site is not a brilliant plan, yet it still seems to pay off even with the moderate number of people that sidestep this disincentive.
There are other ways to associate a brand with your content in exchange for money. The kind of ads that are blocked by adblock are only blocked so trivially because they a delivered in such a disassociated, spamlike fashion.