A reader asks this question, testing the boundaries between physics culture and religious belief:
How hostile do you think a learning institution would be to someone in their Physics department looking at the Horizon problem via the Universe being an Ex Nihilo creation of God, where matter was purposefully set in place and then a God-caused spacetime expansion? (As opposed to the thought experiment of assuming a singularity and a "Theistic or Non-Theistic Big-Bang" requiring another speculation (inflation) to explain one of the shortcomings of the theory.)
— Dean C
Most physicists aren't actually militant atheists, but all of us (whatever our views on religion) have been exposed to numerous "crackpots" who think that they have found major flaws in conventional physics and have a completely new and revolutionary way of doing things. I discussed this pathology here and here. At least 99.99% of time, outsiders making such grandiose claims are totally wrong (or "not even wrong", because their ideas aren't precise enough to be testable), and so we filter out pretty automatically anything which pattern-matches onto typical crackpot-seeming claims and behaviors.
But this is not to say that simply criticizing inflation, all by itself, would get you lumped into the "crackpot" category. Even among respectable mainstream physicists, inflation isn't completely uncontroversial. While most of us believe it is true, this hasn't been established with total certainty.
A lot of the original arguments for inflation (e.g. the flatness and horizon problems) are a little bit philosophical in nature, and it's understandable if you don't find them completely convincing. But it's not just generic arguments like that. Inflation also makes some very specific predictions about the state of the universe after inflation ends, and these predictions seem to match very closely to what we actually observe (as the graph in that article shows). There are respectable researchers (such as Neil Turok and Paul Steinhardt) who have philosophical objections to inflation (not based on religion) and are working on alternatives which may predict the same features in the microwave background. But they are able to do that only because they fully understand the mathematics of inflation and the observational tests that it passes.
If somebody said something like "For philosophical reasons I am skeptical of inflation, and therefore I am interested in exploring alternatives to inflation such as X, Y," and if this person understood the mathematics of inflation (so they weren't just criticizing something they didn't know well enough), and if X and Y were mathematically-precise models with equations (such that even somebody who didn't believe in God could manipulate the equations and work out the predictions of the model), and if there was some hope that in the future, that model could be confirmed by empirical observations, then if all of these conditions are met, I think at most places this would be regarded as acceptable though eccentric. Even if the "philosophical reasons" included some religious considerations.
It would be even better if this person had the ability to "suspend their disbelief" by sometimes having useful conversations with other people that presupposed the truth of inflation, without bringing up their reasons for skepticism every single time. (Because that would make them a more useful colleague, and its scientifically it's an important skill to be able to work out the consequences of hypotheses even if you aren't convinced by them yet, as a way of keeping a open mind and understanding the relationship between ideas.) Such a person would be capable of interfacing with other scientists who don't share his conviction.
(Which is not to say you could actually obtain a research job simply by working on X, Y, since there also need to be a sufficiently large number of other people who think work on X, Y is valuable enough to pay somebody money to do it. In practice, people who work on long-shot alternatives to standard physics also need to work on more conventional topics, in addition, to be viable. There are limited resources and funding in science, and not everyone can be supported. But not getting a job is quite different from being excommunicated as a heretic!)
On the other hand, if X and Y can't be understood without reference to a Creator, and have phrases like "and then God miraculously caused this to happen" in them, or if the model doesn't lead to any mathematically precise predictions that could in principle be tested by future experiments, then this would not be anything like Science as it is traditionally practiced, and it would be dismissed off-hand by almost all scientists as a scientific theory.
And rightly so, because it would, at the very least, involve an enormous paradigm shift in what it even means to practice the scientific method, and justifying such a change would require overwhelmingly convincing evidence. Of course, as a Christian I believe that miracles have happened in history, and that the universe was created by God. But in the field of Cosmology as practiced in Physics departments, the job is to mathematically model the universe using a set of natural processes described by equations.
It's hard to see how "matter was purposefully set in place and then a God-caused spacetime expansion" could, all by itself, be a mathematically predictive theory. Because if the matter was just spontaneously created, there are almost an infinite number of configurations it could have appeared in. Without some physical process or principles to limit it, it could have been anything! And a "God-caused spacetime expansion" must either be described by a set of specific equations like that of Einstein's (in which case, an atheist could also use those same equations, while denying the existence of God) or else it means we (not having access to God's "hidden counsels") simply can't predict exactly how the size of the early universe changed with time. But then how do you get any quantitative predictions for what you see when you point your telescope into the sky?
But if all you mean is that, in the ordinary course of doing science, scientists should not a priori rule out mathematically well-defined hypotheses (such as the fine-tuning of the constants of nature in a way that happens to permit life, or a net nonzero number of baryons coming out of an initial singularity), simply because those hypotheses seem "unnatural" in the absence of an intelligent creator, then I agree with this. Nor, obviously, should a theist rule out the possibility that God might have created our universe using inflation (I don't see why not). Such scientific hypotheses should stand or fall on their own individual merits, as the case may be. It's okay (and indeed essential) to be guided by our own individual sense of parsimony, but we shouldn't be so biased that we rule out sensible models which explain the facts better.
(Incidentally, if inflation did happen, then the hypothesis that the universe just "started off" with more matter than antimatter can't work. Even if there were more baryons than antibaryons coming out of the initial singularity, the universe expanded so rapidly during inflation that the initial baryons would have been diluted to homeopathic proportions. For this reason, physicists generally prefer models of baryogenesis, in which the baryons are created by some specific physical process some time after inflation ends.)