This is a big subject, but there are two basic schools of thought on how to model real-life computers (which I assume you mean -- the CPU is only one part of a computer) with mathematical automata, and they lead to two different theoretical areas -- (a) finite-state automata; (b) infinite-state automata with various restrictions. Both Turing Machines and PDA's are examples of the latter, as are resource-bounded models of computation in complexity theory (P, NP and all that).
The argument for finite state automata is that all computers are inherently limited to a finite number of states, however large (and it is large, like $10^{12}$+, even without the disk, which takes it up to $10^{25}$ or so) because the world is a finite place, at least the corner of it that computers live in. The infinite-state perspective says that's true, but the number of states of an actual computer is so large that modelling it with infinite state mathematics leads to more useful insights on their structure and limitations. Both make some sense, but the infinite-state position is by far the predominant one today, especially with complexity theory. There is some research activity on finite-state models still going on, but the majority of it is concerned with the complexity of smaller circuits and devices rather than entire computers.
As for whether a PDA is a good model for a real computer, that's clearly a question in the latter category -- PDA's have infinite states structured and limited in a specific way. But that way -- a single, simple stack -- is pretty much unheard of in the world of real computers. There have been and still are real computers with built-in stacks, but many of them and they usually have features that exceed those of a simple PDA . Nevertheless, the theory of pushdown stacks has been useful in understanding such computers. Also, mathematical models of target machines for high-level languages invariably use stacks, and again the theory of how stacks work is very useful there for analyzing such models.
So, the answer to your question -- in brief -- is mostly no, the PDA is not generally a good mathematical model of real computers, but it has some relevance. But neither is a Turing Machine, since real computers don't use anything resembling the tape of a TM. On the other hand, both PDAs and TMs lead to useful mathematical models of different aspects of computation in general with many important theoretical and practical consequences.