I can understand their rationale.
Omar's political stance is radical left. So the radical right believe she is un-American because America, they think, should be radical right (self-determination rather than government interference).
In other words, the Republicans think she should love it or leave it and since Omar doesn't love it the way the Republicans want it to be, she should leave...go back to where she came from.
Got nothing to do with the fact that she's black and came from Somalia. It's her radical left-wing politics that rankles the extreme Republicans...not her color.
Lest you misunderstand, I just presented their argument, not mine, for why it was not racist. In fact I think it was just one of many racist indicators from Trump and the Republican Party as a whole.