My understanding has always been that taquitos are made with corn tortillas and flautas are made with flour tortillas. Personally I prefer good homestyle mexican fare (e.g., Taqueria de Mexico, El Sombrero (aka Hat Restaurant)) to good high-end mexican fare (e.g., Maya, Rosa Mexicana). However, comparing the two is like comparing apples and oranges. Coming from Los Angeles, I have yet to taste any homestyle mexican fare in NYC that comes anywhere close to LA. In particular, Las Fuentes (just over the hill from LA) makes flautas that simply cannot be beat.