The answer, I believe, shows just how phony and stupid Panera Bread is. Wikipedia tells me that it was originally called the "St. Louis Bread Company", which is a far more honest name that is bereft of any false pretention and lets people know they're going to a chain that is essentially yet another chain. The new name implies it's mass produced garbage masquerading as something better (cf. Olive Garden).

There is no such thing as "panera" in any Romance language that I'm aware of. As you pointed out, the first part of the word, pan-, is definitely based on the real Latin root panis, "bread", which became pan in Spanish, pane in Italian and pain in French. But the -era? What the Hell is up with that?

Well, Wikipedia tells us that the word "panera" is a word "that has roots meaning "bread basket" in Latin". In other words, they're admitting it isn't a real word but they're trying to say its roots mean "bread basket" in Latin. Except that they don't. Latin words for "basket" include canua, corbis, canistellum (specifically for bread, that one), or nassa. Vulgar Latin added cista, which is from Greek originally and became the common cesta of Spanish and Italian.

So if they knew shit about Latin they'd name the restaurant Canistellum if they wanted to call it "bread basket". But they don't. They're bullshitting everyone, just like they're bullshitting everyone about the quality of their food (apparently - I've never eaten at one of these places).