In addition to the above, you have to remember that the late 1800's is commonly referred to as the Gilded Age (thank you Mark Twain), which was marked by massive monopoly profits and a laissez-faire (government keeps its hands off of business) attitude towards regulation.
So when organized labor began its early attempts to unionize companies and industries, there was an immediate and often violent backlash. The Knights of Labor organized unskilled sweatshop workers, and had virtually no bargaining power with ownership because the workers were so easily replaced with new immigrants. They lasted less than a decade. The American Federation of Labor was more successful organizing skilled workers, but did not significantly help workers' issues in the short term.
In a larger sense, I would say that the American foray into Industrialization and the promise of unlimited riches hurt the organized labor movement. The prospect of workers' rights and empowerment was not something readily embraced at the time. Rather, the vision of Industrialist wealth and maximum profit layered upon further profit helped to fuel the dreams and visions of many. Immigrants who came to America in search of a better life immediately sought the life offered through industrialization and material wealth. The concept of commitment to workers' empowerment and entitlements did not have as much of an allure. The myth of "rags to riches," was a powerful, albeit rare, vision. Individuals were able to cling to the idea that they, too, could make it big and this helped to fuel a constant stream of acceptance of industrialization. It was so strong that when workers' activist movements offered opposing visions of reality, the myth overcame many and the movement's mission was almost doomed to rejection by many.
The most obvious thing that hindered the development of organized labor during this time was violence.
During the late 1800s, it was quite common for companies to bring hired "detectives" in to fight with and/or intimidate striking workers. Perhaps the most famous example of this came in the Homestead Strikeof 1892 where detectives on a barge engaged in a gunfight with strikers dug in on the banks.
Violence of this sort was often tolerated by the authorities, who were generally on the side of the employers.
Another thing that worked against the unions was the surplus of available labor. It is hard to form unions when there are lots of workers who will be willing to take the place of your workers if they go on strike. Since there were huge numbers of immigrants coming into the country at the time, this was another difficulty for the unions.
Overall, then, violence against workers, which was ignored or approved by the legal authorities worked together with demographics to hinder union development.