Yes and no. Boise State has beaten the top teams when they've played them, but they have a huge advantage in that they play such a weak schedule for 90% of their games that they are never battle-weary. Boise's SOS over the past decade averages somewhere in the 90s (of 120 teams). Their strongest SOS in the past decade was something like 74th in the nation (I ran the numbers last year, but can't dig them up right now). In contrast, Nebraska's most embarrassingly weak SOS in the past decade was 54th in the nation, meaning our weakest SOS was 20 spots higher than their toughest.
Bottom line is this - put Boise St. in the Big 12 over the past decade and they don't have nearly the same success. They'll get worn down in an AQ conference through sheer attrition. It's easy to stay healthy when you're playing the equivalent of Div II schools every week. They'll have to go through a conference championship game, adding another layer of difficulty to the mix, and they'll have to scheme against real defenses/offenses every week. No matter how good a staff, when you're challenged every week, the odds of missing something or failing to prepare properly for something goes up quite a bit.
I give full props to Boise State for winning the games they should win. But they have a HUGE advantage over AQ schools right now, regardless of the fact that they're very good.