I think in assessing Aristotle and Thomas we have to distinguish between their science and their metaphysics. Even if the scientific data and conclusions were wrong and now outdated, does that invalidate their metaphysics? Modern Thomistic philosophers such as Feser (e.g. in book such as Scholastic Metaphysics, Aristotle’s Revenge) make a strong argument that the philosophical significance of modern scientific findings can be reinterpreted in a Thomistic metaphysical framework without violating any empirical conclusions about the data. Note that Feser doesn’t think there’s a conflict between evolution and Thomism for this reason, and neither do the majority of Catholics.
In this case, the Thomistic concept that things consist of form and matter (or hylemorphism) is a basic philosophical concept deduced from common everyday experience. It’s in contrast to the atomistic viewpoint assumed frequently today. One of the most common applications is with regards to the human body. Atomism says that my body is only an arrangement of atoms that happen to move together in a coordinated way due to their low-level interactions. If I have a soul, then this is soul is completely immaterial, a sort of “ghost in the machine”. In contrast, hylemorphism teaches that there is a certain overarching principle of unity that governs the behavior of the cells and atoms in the body, making it into a single thing. So instead of bottom-up causation, you have top-down causation or holism. In hylemorphism, my soul is not a ghost in the machine, but the principle that gives this unity itself. Thus, the soul is not completely immaterial, but very closely wedded to the physical matter that makes the body.
Now, this doesn’t mean that Thomism is against the findings of modern atomic physics in any case. It just means that in a Thomistic framework, modern atomic physics is interpreted within a different philosophical framework, that of holism instead of reductionism. While reductionism is simply assumed by many popular science writers and scientists, among philosophers of chemistry and science (and not just Thomistic ones) this is far from being uniformly the case. There are plenty of respectable arguments in the literature to defend holism.
Again, Thomists are not trying to argue for the truth of the pre-modern scientific understanding of physics. Rather, they are arguing for the truth of certain metaphysical principles that Aristotle and Thomas used. In fact, in this particular case some have felt that these principles fit better in light of quantum mechanics, as Heisenberg himself commented in Physics and Philosophy (and @jongarvey and @Eddie like to say). Neo-Aristotelianism is an active movement within professional philosophy of science, not just as an apologetic wing of the Catholic Church.
I certainly agree with you that in light of modern science, we have to be careful and critical in how we are to understand Thomism. This is exactly what pro-evolution Thomists such as Austriaco are doing. But for me, it’s unsatisfying to completely restrict Aquinas’ conclusions to theology alone. The problem is that how Aquinas discusses and understands God is deeply integrated with his metaphysics - for example his idea of God as Pure Actuality. Aquinas’ influence on subsequent theologians - not just Catholic ones but most of the Reformers as well - is immense. If one is a Christian who wants to be aware of and guided (though not ruled) by tradition instead of completely reinventing the theological wheel, there are serious questions about how Aquinas’ doctrine of God (which is basically the orthodox doctrine of God, at least in the West) fits with his understanding of everything else.
