The series of surveys revealed that the company had enjoyed

The series of surveys revealed that the company had enjoyed success more due to the fact that its customers felt limited in their purchasing options than having brand loyalty

A due to the fact that its customers felt limited in their purchasing options than having[who have?] brand loyalty
Wrong.
- due to the fact is not correct.
- Structure is not parallel
- Who have brand loyalty?

B due to its customers feeling limited in their purchasing options than to having brand loyalty
Wrong.
- Not parallel. [due to X than to Y] is wrong idiom.

C because its customers felt limited in their purchasing options than that they have brand loyalty
Wrong.
- "That" refers to what?

D because its customers felt limited in their purchasing options than because they had brand loyalty
Correct.

E because of its customers feeling limited in their purchasing options than because of their having brand loyalty
Wrong. Awkward.

What is "they" referring to in option D the other choices didn't make sense and I picked D but I want to know what is the referent for They..

To answer your question, I searched the definition of "brand loyalty"

According to Wikipedia: "Brand loyalty is where a person buys products from the same manufacturer repeatedly rather than from other suppliers"

Who have brand loyalty? Only customers do. So "they" clearly refers to customers.

Hope it's clear.