There are a number of ways in which this happened. Let us look at two of the more important ones.
First, the new immigrants were ethnically and religiously different from the bulk of Americans. The new immigrants were typically from Southern and Eastern Europe. They were Jewish and Catholic. These factors (with the exception of Catholicism, as there were many Catholics already in the US even if their religion was suspicious to many) made the new immigrants seem threatening. This led to tensions between them and "natives."
Second, many of the new immigrants were politically radical. This was a time when Europe was rife with anarchist and communist/socialist sentiment. Many of the immigrants subscribed to these ideologies. This made them seem dangerous to many Americans, thus heightening tensions between the immigrants and the people already in America.