I think they can indeed be a bit intimidating (and I've been using them for more than 20 years, almost half of which I've been living in Europe).
The first and most obvious potentially confusing thing is that your destination may not be named as the train's destination. I'm thinking about if I'm taking a train to an intermediate stop. i.e. the train's destination is Nice, but i'm going to Cannes. The "big board" in the station does not list all those intermediate destinations -- so when I look up there looking for "Cannes", I won't see anything. Now if I know my geography a bit and am paying attention to the number of the train listed on my ticket, I can figure it out. (Obviously these things are old hat to me now, but I'm thinking of them as someone encountering this on one of their first attempts.)
The designation for my car and seat may not be clear to me if I don't know the words for them; and indeed even if I have interpreted them correctly (or believe that I have), I can still come on board to find someone in my seat or several people in the seats that are supposed to be for me and my party. With their luggage up above taking up all the space that is supposed to be for our luggage. This happened to me and my parents on our last trip. While it was fine, because I speak French and let the kids have it who had taken our seats, it was an additional stress, because arguing with the one kid sitting there (the others had gotten off to smoke a cigarette during the station break, natch) and the delay in getting me, my parents, and our stuff in the compartment meant we took up space in the corridor much longer than was normal, causing frustrations for the other travelers behind us trying to get to THEIR seats. (Imagine them finally getting in and maneuvering their bags aside enough for me to get ours up - the whole thing was a huge PITA).
If I don't know there are two sections of the train station (as there are, for example, at the Gare de Lyon), I might find that confusing, too.
If I don't have military experience and am new to Europe, I might find myself thrown off by the use of 24-hour time. That shouldn't be a big deal, but even a "smart" person like myself has messed that up once enough to miss a train by 2 hours!!
I may be confused about composting my ticket -- or not as the case may be, I may not understand how to retrieve my pre-paid ticket from an unmanned machine with my signature-only credit card, or I may have a very long line ahead of me for the manned line (and be nervous about whether the ticket salesperson speaks enough English or if I can make myself understood).
I may be on a train happily scooting along, when something happens and we stop for a while -- if I don't speak the language, I won't understand the descriptive announcement.
I may be confused about understanding when to get off my train if it's not the end of the line. Will I be prepared, be able to get my bags, and step down in time?
A lot of these are not really issues for me personally anymore. But I can empathize with someone who might find it a bit intimidating to use a European rail system, yes.
For assistance, I would recommend the sites of the man in seat 61 and paris by train, trying to learn as much you can about the terms for various railway words in the languages of the countries you're visiting, allowing yourself time at the train station, and keeping your eyes and ears open. And hoping for friendly fellow passengers in the case of a stoppage or delay that causes you to have to get off the train and wait for a bus, or get another train, etc.