What's the difference between a flauta and a taquito?
If I remember correctly, flautas are made with a softer flour tortilla while taquitos are made with a harder corn tortilla. Both are filled with similar fillings and then wrapped and deep fried. 

However, you can oftentimes find taquitos made from flour tortillas and flautas made from corn tortillas...so what's the deal? There is another differentiation: size. Flautas are often longer than taquitos, as taquitos are made from taco sized tortillas, while flautas are made from burrito sized tortillas. 

Another little tidbit if you go to a fancier Mexican place: flautas are often narrower on one side to create a funnel shape. But this is not common in your standard places.

TL;DR; They're oftentimes the same thing