Union dislike
I agree with Timebuilder. A lot has to do with salaries. Employee compensation is one of the biggest expenses for companies. It is axiomatic that to raise profits you cut expenses. Therefore, if a non-union airline can attract pilots of equal quality as a union shop and pay them less, it has cut expenses. Not to mention fewer benies.
Many companies oppose pay according to scale. They'd prefer to pay, or not pay, according to merit. Let's say we have two pilots. Somehow, the company feels that Pilot A, who makes himself/herself available for extra reserve and comes in to work in the training department on days off is more valuable than Pilot B, who sits on interview boards on days off and chairs the United Way committee. Let's say both are 747 captains. Obviously, both pilots are valuable, but there is no objective criteria to evaluate merit. With scale, both are compensated equally. Fairly? Weigh it against the industry.
Now, once again, the other point of view might be my dad's business philosophy. His business was dirty and hazardous and he regarded his employees to be a valuable resource. He wanted to pay them better than any union contract, but was stymied by that when he had the union.
Power. I will not say that companies "oppress" workers. That sounds too much like Karl Marx or Hegel, perhaps. But many businesses and companies take unfair advantage of their employees and their cooperative nature, and single out certain employees or groups of employees. For example, I worked in a lawfirm in which the principal attorney habitually kept staff late and heaped unreasonable amounts of work on them. Staff worked long hours and for no extra pay. The principal got away with it because she considered staff to be "professionals" and exempt from overtime. Not that a union would have been practical in our small lawfirm, but if we could have spoken up with one voice we might have been able to combat this abuse.