I doubt making a Soyuz and throwing it away is cheaper than building an F9 and reusing the first stage and booster 10 times. At that point the second stage would have to cost almost as much as an entire Soyuz stack.

Making a Soyuz is really, really cheap. Something around 5 million dollars for the rocket. Most of the cost in a Soyuz launch isn't from building the rocket.

If it is the case then we will see SpaceX charging NASA less than a Soyuz launch amortized over the number of passengers per launch. But in 2021 it still isn't the case.

So you're arguing it's cheaper in the case where nobody openly knows Roscosmo's numbers, nobody can obtain the services at those numbers, then comparing the cost at the FACTORY for Soyuz to the price of LAUNCH for SpaceX - before accounting for using the same rocket TEN TIMES - and still claiming Soyuz is cheaper?

Edit: Parent filled in data below, it looks like Soyuz in cheaper. :)

We actually can optain the numbers. Roscomos is a public agency. They buy the rockets from the Progress join venture, and a public the exact cost of both the rocket and the launch. The cost of only the rocket is around 5 million dollars.

The total cost in 2018 for a Soyuz launch to Roscosmos is 3.5 to 4 billion 2018 rubles, which is around 20-23 million dollars per seat.

The cost is kind of at the factory because Roscomos partially builds some systems of Soyuz. But in the end it costs Roscosmos 20 million to put someone into space using a Soyuz, and it costs NASA 55 million to do it via SpaceX.

I'm comparing the cost of launching an astronaut to the ISS. For Soyuz, since the rocket is not reusable, this is the cost of the rocket plus capsule plus payload plus préparation, tracking, etc.. For SpaceX, it is just the cost of their launch. Soyuz is simply so well engineered that it still is cheaper, even though the SpaceX rocket is reusable.

> even though the SpaceX rocket is reusable.

As I pointed out already, the original NASA contract was signed long before SpaceX recovered a single core. Tose prices don't take into account reusability at all. SpaceX already has two pre-flown crew rated first stages ready to fly again. NASA has recently approved using them, and refurbished capsules, for upcoming missions. The cost calculation today is nothing like 2014 when SpaceX signed Commercial Crew.