Turns out my suspicions were correct. There are small, if distinct, differences between the two Mexican specialties. First, while taquitos are generally made with corn tortillas, flautas (Spanish for "flutes") are usually made from rolled-up wheat flour tortillas.
Second, in certain regions, taquitos are often the petite-sized, appetizer variety, while flautas are the lengthier form of the dish, made from burrito-sized tortillas and served as part of the main meal. However, in occasional situations and some places, the two terms are used interchangeably.
Source: Flickr User the.dugger