Not true at all. The Imperium is decentralized because of their own incompetence and the intrinsic difficulties of managing an empire of that size, not because of any ideological opposition to centralization. This is not a valid argument against charges of fascism.
Not to mention that the evidence of fascism is overwhelming. For example, let's look at some common fascist traits.
- Rejection of Modernism/Support for Reaction: Fascist ideologies may use the trappings of modernism, such as industrial technology, but they reject the values they associate with modernity such as reason, egalitarianism, democracy, etc. It shouldn't need much explanation of how this applies to the Imperium, technological innovation is extremely heterodoxical at best if not outright heretical. And it's not like social movements are likely treated much better.
- Irrationalism: Fascists support action for the sake of action, they reject contemplation or intellectualism seeing it as "womanly" and thus weak. It can't be denied that the Imperium supports Irrationalism, "an open mind is like a fortress unbarred" etc.
- Rejection of Difference: Fascist movements rely on the fear of difference, the outsiders must be kept out if the organic body of society is to remain pure. The Imperium is all about this, from their meme-tastic hatred of aliens to their treatment of mutants they aggressively reject any difference. With the exception of Abhumans and Space Marines, but this does not make them less fascist, hypocrisy is perfectly normal in fascism (see: Hitler allying with the Japanese).
- Obsession with the Plot: Fascists need to drive the population into a frenzy to justify their constant purges and crackdowns, because of their Rejection of Difference the plot always has an ethnic tinge. For the Imperium this manifests in the form of their paranoia about Chaos, admittedly Chaos is an actual threat but the Imperium undeniably makes it worse by accusing people of heresy at the drop of the hat and making people's lives worse. So I'm counting this as a manufactured threat, a more competent/benign civilization would resist Chaos much more effectively.
There are more common traits of fascism but I think this illustrates the point quite nicely. The Imperium of Man is undeniably fascist, arguing otherwise is incorrect and baffling. There's a reason that they were called the "Cruelest and Bloodiest Regime imaginable", they aren't the heroes and just because the other guy is a monster doesn't make that less true.
That's why I love 'em, they're hideously dark by the standards of a sane universe. But there is a difference between loving them as a character and excusing them, we should never approach the latter.