There are some great answers in this stack exchange post: https://blender.stackexchange.com/questions/7298/why-is-it-important-to-apply-transformation-to-an-objects-data

Quick answer: Because if you don't, you may get unpredictable results when modifiers (such as rigs) 'handle' your meshes later in the pipeline.

Sometimes you won't want to apply scale or rotation if you want unqiue effects. Using an empy with an array is a good example or when using constraints is another.

When you are starting out I would say it is "The SAFE thing to do"

These helped me until I was more comfortable knowing what tools did more comfortably:
1. model with your object's origin at the world origin with the line of symmetry dissecting the world origin
2 model with Rotation and Scale set to 1 (or applied to 1) when using modifiers that you are still learning about
3 break these rules at any time when messing around or learn what they do and test what behavior they provide. Sometimes you just gotta be a Mad Scientist to learn this stuff better.