According to a recent Pew survey, Americans perceive Jews more favorably than any other religion: 35% have a very or somewhat favorable view of Jews, 58% have no opinion, and 6% have an unfavorable opinion. That’s a 28 point “balance of opinion” between favorable and unfavorable. Mainline Protestants ranked second, with a 20 point balance of opinion.
Evangelical Christians had a 2 point balance of opinion in favor. However, most religious persons have a positive perception of their own religious group. If you remove the opinions evangelical Christians had of themselves, then they wound up with a negative 14 point balance of opinion.
Finally, people apparently tend to have a higher opinion of religious groups where they know someone that belongs to that group. Thus, Muslims and atheists fared poorly on this survey, probably in large part because so few Americans know an actual Muslim, or a real live atheist. However, atheists tend to have negative views of other religious viewpoints.
Link to the survey on the Pew website