I'm a civil engineer, but you seem to be interested in aeronautical engineering (as far as I can tell from the example you gave), so my answer might not be applicable to your case (but it probably is).
Basically, any and all loading is calculated with a safety factor for ultimate limit state checks. However, the value of that safety factor may be different for different types of loads. The Brazilian code for reinforced concrete bridges, for example, defines that permanent loads (self-weight and dead loads) must have a safety factor of 1.35, while live loads need 1.5, and wind needs 1.4.
There are secondary safety factors, such as if you are testing the summation of different non-permanent load types: for instance, heavy traffic probably won't cross your bridge during hurricane-strength winds, so you might make two tests: one with heavy traffic as the primary load and wind as a secondary load (with a "reduced safety factor"), and another with wind as the primary load and traffic as secondary.
For some checks under exceptional conditions, certain load types might even be given a safety factor of 1.0, that is, no safety factor. Also, if doing serviceability checks, there usually are no factors.