What obstacles hindered the development of organized labor in the late 1800s?

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.