Identitas does not translate straightforwardly as 'identity'; it's perhaps important to insist on this because a lot of people seem to be under the impression that Thomas Aquinas is committed to the position that everything in God as identical to everything else. Identity is a relation that is at least minimally (1) reflexive; (2) symmetrical; (3) transitive; (4) antisymmetric. (I say at least minimally because, as far as I am aware, we have no non-circular account of identity; these four characteristics leave identity indistinguishable from equality, but there are good reasons to deny that equality is always identity, although identity may be one kind of equality. Intersubstitutability is a plausible fifth characteristic, but it very quickly runs into all sorts of difficulties and puzzles; indiscernibility runs into different troubles and may presuppose identity in any case, for reasons too long to get into here.) But identitas is only transitive and antisymmetric when certain conditions are met. In particular, on Aquinas's account, these things arise only when two things are the same secundum rem and secundum rationem. If two things are idem secundum rem they can be referred to as one thing, but if they are still idem secundum rationem there will be contexts where transitivity and antisymmetry fail. For instance, the road from Thebes to Athens and the road from Athens to Thebes are the same secundum rem, because they are the same road. But they are different secundum rationem, and therefore there are ways in which they are not equal, and there are relations and properties that they do not share (e.g., one may be uphill and the other downhill, and one may be the route you follow to visit the Grove of Akademos while the other is entirely the wrong direction) and the fact that they share some things doesn't imply that they share everything (for instance, they might not share modal properties). Nor does it suffice to response that, say, the Athens-Thebes road is uphill traveled one way and downhill traveled another; that just says that they are the same secundum rem, which was already conceded; we still have to deal with the fact that they are obviously different secundum rationem, which the response, in recognizing that direction makes a difference at all, has itself just conceded.
Part of the reason for this disparity is that we draw our notion of identity (which, we must recognize, is actually in some ways very obscure and not at all as precisely characterized as some seem to think) from a very particular set of uses. But Aquinas couldn't do that. Rather, he's taking a very broad and often colloquial idea, idem, and making distinctions with regard to how it is used, in order to make it more precise. Identitas can indeed indicate something reflexive, symmetric, transitive, and antisymmetric. But sometimes it indicates something even weaker than either an equivalence relation or a partial order. Idem is not used univocally in every situation.
