Well the only way you would have a problem is if you tried to enter the US. Flying over it is not a concern for you. Emergency landing is another thing. If the plane did have to land then by all means don't try to get through US Customs. So you should be fine for the flight.
Now once you are in Mexico, and your passport is in order, you should be fine going the Mexico customs. They do not have scanners or anything that will pull up a red flag at the airport so you should be fine there.
Now IF you get arrested in Mexico that's a whole other deal. The most important thing about your question that you have to ask yourself if "how bad is US looking for you" What I mean is are you on the 15 most wanted fugitive list? or are you mixed up in the other 2.5 million people with outstanding warrants in California. There are soOOO many people with outstanding warrants in the US that you would really need to be on a hot list for it to be a problem for you Other than the fact if you really screw up in Mexico, piss alot of people off and they run your through the states and find the outstanding warrant.
You can also go to the state website that you think you have an arrest warrant in and really find out if you have a warrant out for your arrest.
I found this on the web
Also, the Marshals Service is the primary agency responsible for tracking and extraditing fugitives who are apprehended in foreign countries and wanted for prosecution in the United States. The U.S. Marshals Service, which has statutory responsibility for all international, federal and state extraditions, sees to it that there is no safe haven for criminals who flee the territorial boundaries of the United States.
The U.S. Marshals Service defines international fugitives as, fugitives wanted in the United States who have fled to foreign countries to avoid prosecution or incarceration. Interaction with numerous law enforcement agencies and representatives of foreign governments is daily occurrence. The U.S. Marshals Service is constantly networking to establish and improve relationships with foreign governments to enhance its ability to apprehend fugitives seeking refuge in foreign countries.
In 2003, the U.S. Marshals Service opened field offices in Mexico City, Mexico; Kingston, Jamaica; and Santo Domingo, Dominican Republic. The focus of these offices is to coordinate U.S. Marshals Service fugitive investigations with law enforcement in each country to coordinate arrests, extraditions, and deportations. In addition, the U.S. Marshals Service develops on-going training programs for these countries in fugitive investigation techniques and officer survival
The U.S. Marshals Service is responsible for carrying out extraditions to the United States from foreign countries and for supporting extraditions to foreign countries from the United States: a complex task involving coordination among the Department of Justice, Office of International Affairs; the State Department, foreign governments, U.S. embassies, and U.S. Marshals Service district offices. The extradition process involves country clearance, threat assessments and security arrangements, travel arrangements, and any necessary medical assessment and accommodations. In fiscal year 2008, the U.S. Marshals Service coordinated 857 extraditions/deportations involving 60 countries.