Let's apply that to the Herpes Virus known to be risk factor for cervical cancer. There is a greater than 1% you catch the disease.
But, the risk you die from it is lower, maybe in 10,000? (Even the people who research it probably would have a hard time giving an estimate within an order of magnitude).
So would a parent give it to their child at 1 in a million? Assuming every child is given this vaccine 10M+, there would be around a dozen known fatalities. Both parents and FDA would probably have big problems with this.
(Disclaimer: this a hypothetical using a known condition but with made up facts. I take no position on "the vaccine debate" here.)
Also suppose you have a 1% chance to catch and die from a disease without the vaccine.
You would take the vaccine every time.