Employers resist unions for a number of reasons, but the biggest reason is that unions force employers to have less control. With a union, workers can organize, gain power, and limit the flexibility of the employer and the rules the employer imposes. Individually, workers can't do much to change the policies of the employer or fight employer abuse, but as unions they can. Employers resist this challenge to their authority.
Unions are mainly opposed because the employer sees them as detrimental to the effectiveness of the company. Union contracts make it difficult for employers to make quick, major decisions or changes, and unions can limit the turnover rate of employees so that employers can't hire as many people and fewer workers will be able to get jobs. Union support can also lead to restrictions on firing employees, even those that perform poorly. Unions also can remove the profit incentive, so employers that deal with unions have no reason to try to keep costs down.
Unions can force the employer to implement policies that the employers see as detrimental to the company. For instance, unions have the ability to engage in collective bargaining. Even then, though, employers are hesitant to bend to the will of the collective workers. Most employers are anti-union, and some even punish workers for joining unions with harassment, interrogations, and surveillance about union activity.