Ah. That's is where this thing went off the rails. No, sorry. A flagship product is a companies top product. The one with all the bells and whistles, the one that leads the rest of the pack.
The term "flagship" comes from the days when ships sailed together. The lead ship was the flagship. And so too it is with products, which it why marketing co-opted the term. Even a company like BMW has one flagship product. The 3 series, for example, is a very nice car. It's not the flagship. Armani is an elite name in the fashion world, but Emporio Armani is the flagship. Armani Collezioni and other Armani labels are a rung+ down in the product lineup.
This is not me determining what "flagship" means in reference to consumer goods, it's the universal definition.
Now you may personally regard all iPhones as great. That's fine. But from a marketing and sales perspective, the 5S is not a flagship product in 2016. The iPhone 6SE is a huge seller and may even help Apple bridge the revenue gap this quarter. But it's not the flagship product.
If you don't understand this now you will after you take a few business classes in college.