This question stems from a misunderstanding that I also held personally for a VERY long time, and only just recently comprehended: A "radio frequency source" is not the same as a photon in the radio part of the frequency spectrum. These systems do not rely on hitting the fuel gas with photons.
Your intuition is 100% correct that photon bombardment at radio frequencies would not make many ions. A photon from the radio part of the spectrum (call it 5 mm wavelength) will contain 0.000248 eV of energy, while the energy required for ionizing xenon (a common electric thruster fuel) is 12.13 eV. There's a bunch of other complicated dynamics with gas-phase photoionization like excitation lifetimes and interaction cross sections at different wavelengths (which, at radio wavelengths, are vanishingly small - we use it for communication because it goes right through quite a bit of matter without interacting at all), but you can get the sense of the situation just from the dummy math: 12.13 / 0.000248 = 48,912 radio wavelength photons that would need to hit a xenon atom simultaneously to ionize it. Simultaneously, here, means "within the excitation lifetime of the initial excitation from the first photon that hits" which for most materials and most photon energies is on the order of a few nanoseconds to a few femtoseconds, unless the photon has an energy level resonance with the atom or molecule it is hitting. Anyway, we are usually lucky if we can get two photons to hit the same atom at the same time. Nearly 50,000 ain't gonna happen.
So, what gives with this RF source thing? Well, there are other things that can oscillate at the same frequencies as radio waves, namely electric fields. This is what people are actually talking about when they refer to RF plasmas or RF power sources: they are using an AC electric current, except that instead of switching polarities at 60 hz or 50 hz like your wall electrical socket, they switch polarities at khz to Ghz, like radio waves. Probably the most common frequency for plasma generation is 13.56 Mhz - if this was a photon frequency, that photon would be a radio wave, hence they are called "radio frequency" oscillations. But, it's not a photon.
The way this actually works to generate a plasma is to make electrons dance. As the polarity of the RF source switches, an electron will feel an electric (or magnetic - either will work, just different configurations) field that pulls it first one way, then another. The amount of acceleration that the electron can pick up during each oscillation is determined by the voltage for any given frequency - higher voltage, faster electron, more energy added to the gas. Free electrons in the gas will hit neutral molecules, and if you make the oscillation voltage high enough, eventually those collisions start to happen with enough energy to knock electrons off the neutrals, and create more ions. There are some factors that impact the rate of ionization, such as recombination, energy absorption into the plasma, and energy loss through de-excitation (light emission) and thermal collisions, but fundamentally if you keep pumping in power from these RF oscillations, and the voltage is sufficient, you will end up with a lot of free electrons, which will maintain a very highly ionized plasma.
These systems have a few dynamics that should be noted:
First, you need free electrons to seed the system - the voltages used are way below the voltages required for an electric field to just yank electrons off of molecules, so the only electrons that really interact with the oscillations in field are those already out in free space. This means that a perfectly neutral gas cannot be turned to plasma by an RF source. In practice, there are almost always a few free electrons in a gas because of cosmic rays that are always passing through, and DO have enough energy in single photons to ionize an atom in free space (some have enough energy in one photon to flip a bit in a computer!). But, if you get the gas thin enough (reduce its pressure quite close to vacuum) there are not enough atoms in a given volume to get hit by these rays, and you might need to supply free electrons independently to spark and maintain the plasma, using a cathode of some kind. And, if the gas gets really thin, you start having electrons make it all the way to a grounding surface before they hit anything (i.e. the mean free path becomes long compared to the oscillation length or the physical dimensions of the plasma chamber) and electrons are just oscillating their way through free space until they hit the walls - no way to start the chain reaction of ionizing and freeing more electrons to go make more ions, so you can't spark a plasma at all. So there is a lower bound on operating pressure for these systems.
Second, the ions (once you spark the plasma and have ions) in the system are barely affected at all by the oscillating field. Ion masses are thousands of times as much as the electron mass, so they are thousands of times slower to accelerate in an electric field. Thus, if the oscillations are fast enough, the positively charged ions barely get moving at all before the polarity has switched, and starts pushing them back the opposite direction. They accelerate through so little of the potential field during each oscillation that almost none of the energy ends up in the ions and nearly all ends up in the electrons. This is useful for two reasons: First, it means that the electrons will always have very high relative velocity to the ions, which is why the impacts are energetic - if they danced at the same speed in the same field, then they would always be moving in parallel and the electrons could not ionize the atoms. Second, it means that an applied DC field across the plasma can extract the ions over time - because the oscillation has almost no net effect, the ions will drift almost entirely under control of the DC bias, which is used in processes like sputtering and plasma etching for semiconductor fabrication to direct ion bombardment at from a plasma at a target.
So, yeah, your thinking was right about RF photons. That's just not what they are actually using.
