There are three types of throws: mixup, punish, and neither. You should only throw if it is a mixup or a punish, never otherwise.
A punish is certain to work - it will hit during the startup or recovery of an opponent's move, and as such has a 100% success rate. Unless another 100% option would be more powerful, always throw here.
A mixup isn't certain to work, but if your opponent has clear patterns then you can utilise that to influence your decisions. For example, they might always throw after you crossup with an empty jump, giving you a free yomi opportunity by simply empty jumping over them! Also, some players will always throw on wakeup vs lum's whiffed crossup roll.
The ideal pattern of throws vs other options is based on two things: expected value, and the opponent's habits. If an option is three times as good as a throw, then you should do it three times as often as a baseline, then adjust for how often your opponent expects it - if they expect it too often then do it less, and vice versa!
For example, if your opponent always yomi counters then you should always go for a combo, and if your opponent always blocks then you should always go for a throw. If you throw too often then you get yomi countered too often, and if you don't throw enough then your opponent will give you fewer openings to attack, hence there being an ideal point between the two.
If a throw is neither a punish nor a mixup, then it's possible for them to "fuzzy guard" against it - this means that they wait before they start blocking, because you threw at a time when you couldn't possibly hit them with anything else. The way to beat this is to delay such throws until they line up with another option, creating a mixup. Unfortunately, this gives the opponent an opportunity to escape, counterthrow, or hit you first.
The short answer is that you shouldn't throw in such positions, but it's possible to adjust it so that it's only risky instead of always a mistake, which I'll explain by example.
By far the most common example of a fuzzyable throw is if you throw on your wakeup. This beats two uncommon options from your opponent: a whiffed meaty (if you know they often mess up timing), or blocking (if they expect and want to punish a reversal, otherwise they would safejump).
In the case of a whiffed meaty, they already made a mistake and it's their fault, but in the case of a reversal they can adapt: they know the earliest moment you can start the reversal (because it's on wakeup), and how long the reversal's startup takes! These are the two requirements to fuzzy guard.
So they can yomi counter until the first moment a reversal could hit, thus defeating the throw option while still defeating the reversal option. This can easily be countered by just delaying the throw until the reversal would hit, forcing them to actually guess, but leaves you vulnerable to being hit by a meaty before you do anything. You can also just run away if they're fuzzy guarding.
A second example is immediately after Argagarg or Midori's ground supers - they are free to act, and if they saw that you were doing nothing then they now know the earliest any of your moves could land! As such, should they choose to fuzzy guard then an immediate throw will always lose, as they are still yomi countering. A delayed throw will catch them once they start blocking, forcing them to dedicate themselves to a decision.
In short, a throw on wakeup is such a bad idea that you need to consider the nature of frame data to make it into a mixup, while still leaving yourself vulnerable. It's still worth including in your reportoire, but only if you have an unreactable reversal, and only rarely versus anyone who handles it correctly.