I don't and the reason is, as you mentioned, if you have a leak, you are less likely to notice it until it's too late (floor damage). This is especially true if the toilet is above a crawlspace or above a finished ceiling. However, it's okay to caulk provided you know you have a good seal and there is no wobble in your toilet. A good way to test is to tap the sides of the bowl with the flat of your palms and see if there's any movement.
Let me know if you have any questions (i'm a master plumber).