The Tortilla Difference
Most of the time Flautas, which mean "flutes," usually refer to a flour tortilla that is rolled up around a filling and deep fried. A Taquito is a corn tortilla rolled in a similar fashion with a filling of beef, chicken or cheese and fried until crisp. Sometimes the Flautas are rolled to be narrower on one side then the other to create a long, narrow cone shape. But the main difference is that usually Flautas are flour torillas, and Taquitos are made of corn tortillas. However, you can also find Taquitos made from flour tortillas and Flautas made from corn.
The Length Difference
In some areas of Mexico the Flauta and Taquito are determined by size. the Flauta is very long, made from a burrito-sized corn tortilla. They are very long and thin and are usually served as a main dish. Taquitos on the other hand are the shorter versions usually served as an antojito or appetizer.