Learn Russian: Почему ты пользуешься её маркером?

This is a special rule for the 3rd person possessive pronouns (его, её, их). Unlike words for 'my' or 'your', these words never change their form to match the case, gender, or number of the noun they describe. They are completely frozen!

Why do we say маркером instead of the accusative case for a direct object?

The verb пользоваться (to use) always requires the noun that follows it to be in the instrumental case. You can think of the Russian logic as doing a task by means of or with that object.

If I wanted to say 'Why are you using YOUR marker?', would the word for 'your' also stay frozen?

No, 1st and 2nd person possessives (like мой, твой) and the reflexive свой DO change to match the noun. To say 'your marker', you would need the instrumental form: твоим маркером (or своим маркером). Only его, её, and их are indeclinable.

Is пользуешься related to the noun польза?

Yes! Польза means 'benefit' or 'use'. The verb пользоваться literally means something like 'to benefit oneself with', which helps explain why it is a reflexive verb (ending in -ся) and why it takes the instrumental case.