This is a touchy and complex issue. Certainly, when one lands at a United States international airport, there is a difference seen in how people from foreign countries are treated and United States citizens are treated. Different lines for different designations help to bring this out. I would not argue that this is bad or good, but it is a difference. I do think that there is an attempt to not have this reflected as good or bad, but sometimes, it comes out as definitely one or the other. There are times when this is evident in the manner a U.S. customs official rifles through the luggage and belongings of someone from another country, and the looks and questions rendered at what is present.
Yet, when one leaves the airport, I think that there is not an outward or institutional difference in how foreigners are treated and how United States citizens are treated. There are no "identification cards" that have to be worn or some type of designation that says "Foreigner" vs. "Citizen." From an institutional set up, there is the equality that is afforded to all people.
Having said this, I believe that your question might go to something more fundamental. The question being in America, is there a difference in how we treat people we perceive to be United States citizens and those we perceive to be from another country? I think that the recent immigration debate, the passage of laws in states like Arizona and Alabama that represent this, as well as some of the tone and timbre of recent events (the Sikh Gurudwara shooting in Wisconsin last Sunday) are all reminders that there might be some level of differences that are faced by those from other countries and those who are "perceived" different that the standard understanding of those who are "United States Citizens." There might just be some type of perception based bias that enables one person to be seen one way and another to be seen in a different one. Proving this will be challenging. Yet, I think that if one sorts through the different items that are present in the national dialogue, it does become evident that what is seen as "different" can be treated in that manner.