Well... bear with me and I'll try not to throw a dissertation-length explanation at you :)
Rome in the days of Seneca and the other major Stoics was far from having a single unified religion. There was a "state religion" following the co-opted Greek pantheon we all learn about in school (Jupiter/Zeus at the top, etc.), but that's far from the whole story. I've got a book sitting next to me right now which just provides a survey and nutshell summaries of the important traditions and major concepts, and it runs around 300 pages; "religion" in the Empire was a huge tangled collection of monotheistic groups, polytheistic groups, pantheistic groups, arguably atheistic groups, and a vast cobweb of cross-pollinations between Roman, Greek, Egyptian, Jewish and Christian traditions.
So a short answer to one of your questions is: "yeah, they had monotheism, but also they didn't".
As to Seneca and the Stoic view: the Stoics like to toss around the word "λόγος" (Logos). But every other philosophy and practically every mystery religion of the day also used the term (plus it got co-opted into Christianity early on), and though the intended meaning is similar in a lot of cases there are also crucial differences. Plus, λόγος and its root λέγω are extremely overloaded to begin with even in everyday Greek. Though you'll often see the basic translations as "word" or "speak", the original concept was "gather", with a further sense of "count/enumerate" (an artifact of this meaning in modern English is "catalogue": καταλέγειν/"count" gives κατάλογος, the list of things counted) and "order/arrange", and from there you can dive off not only into gathering words but also gathering thoughts, and off into much more abstract ideas such as repetition/succession of things or events.
So λόγος can embody a huge number of concepts, but within the context of Stoicism a good approximation is of an all-pervading rational order in the universe, exemplified by the succession of events under natural law. You will find Stoic philosophers who identify this with a god or gods -- typically Jupiter/Zeus -- but it can be difficult to figure out whether they're doing that because they really believe it, or because (as was common at the time) they were simply trying to tie into or co-opt already-familiar ideas, because what they meant by λόγος was something quite different from the personal, corporeal gods of the Roman state religion.
Ultimately, Stoicism -- if it's theistic at all -- is pantheistic, because λόγος by its all-pervading nature must be everywhere and in everything. And since the ordering of things in nature follows rational, predictable principles they argued by analogy that λόγος, the source of those principles, must similarly be rational. They also argued that it must (as a consequence) be deterministic; and thus Stoicism advocates acceptance of things as they happen. To the Stoic, this is the only real choice: to fight, pointlessly, to turn the course of events one way or another, or to accept and make peace with things as they are, and devote yourself to philosophy and reflection and the life of the mind. Even if you can't improve the lot of society, you can improve yourself.
So questions of "fairness" don't really come into it; what Seneca's trying to get at is not that lifetimes have been allotted by some intelligence to serve some purpose, but that so many people waste so much of their lives on a fight they cannot possibly win and end up neglecting the one thing they can genuinely do to improve themselves and find contentment.