Why did the community make the Scottsboro boys feel unwanted?

Well, the short answer is that the Scottsboro boys were young, black males in 1930s Alabama during the Jim Crow era, and they were accused of raping two white women. Life in the south was highly segregated and the civil liberties of blacks, especially young black males, were regularly abused. But more background needs to be provided to understand the full picture of their arrest and the legal battles that ensued.
The nine were "hoboing"—a common practice during the Great Depression when people (usually poor) would ride in empty train boxcars—on the Southern Railway line between Chattanooga and Memphis, Tennessee looking for work.  In one of the freight cars, there was a group of young white males. A fight broke out between the two groups resulting in the white teenagers being forced from the train. They immediately wired ahead and reported what had happened. The train was searched in Paint Rock, Alabama by local police and nine black youths ranging in age from 13 to 20 were arrested. Only four of the suspects knew each other.
The assault charges quickly became rape charges after two white women, Victoria Price and Ruby Bates, accused the nine of raping them. At that time in the southern US, a black man accused of raping a white woman invariably received the death penalty, so the fact that the nine youths were charged made international news and brought a spotlight to the realities of the post-Reconstruction south.
But Victoria Price and Ruby Bates lied. The Scottsboro boys had not raped them. Why would the women lie? At the time, both women were unemployed and riding the train to look for work. To avoid vagrancy and morality charges (a thinly veiled accusation of prostitution), they concocted the story to protect themselves.
The Alabama National Guard was called in to protect the nine accused as they waited for trial. After lengthy legal battles over the course of several years, four remained in prison while four were freed based on the same body of evidence (one of the accused was shot during a prison escape attempt). In 2013, they were all legally exonerated for the crimes by Alabama governor Robert Bentley.
In the end, the Scottsboro boys could not have been in a worse situation. They were poor, black youths in the Jim Crow south of the 1930s and accused of raping two white women. Given the circumstances of the time, there was little chance that they would receive a fair trial (which they did not) much less any sympathy from the local community.
http://www.encyclopediaofalabama.org/article/h-1456

https://www.nytimes.com/2013/11/22/us/with-last-3-pardons-alabama-hopes-to-put-infamous-scottsboro-boys-case-to-rest.html