In any case, if you want to measure hate over time, you're best bet isn't surveys but crime reports. Anti-religious hate crimes have been broken out and reported for years and we have good data for 1996-2012. Here are the trend lines for all the sub-groups.
Hate is up for catholic, atheist, and multi-religious categories. Everybody else is flat to down. As always, anti-jewish hate crimes predominate the numbers but they've got the best trend line of the bunch so maybe in a few decades the jews won't be number one anymore. I'm sure they're looking forward to it.
The muslim trend line is generally flat except for a 9/11 related, one year bump (481 incidents). Most of that went away but the baseline moved up from around 30 incidents a year to perhaps 140 give or take with arguably a slight down trend between 2002 and 2012. This is not the picture of growing anti-muslim persecution the article hints at with its talk of a recent bias crime spike.
9/11 is not the time for a story hook of anti-muslim bias that isn't even accurate.