Here are two sites with the results of research on nipple confusion.
The American Journal of Pediatrics concluded: "Breastfeeding duration in the first 3 months' postpartum was unaffected by pacifier use."
The European Journal of Pediatrics reported the following conclusion, "In our study population fluid supplements offered by bottle with or without the use of pacifiers during the first 5 days of life were not associated with a lower frequency or shorter duration of breastfeeding during the first 6 months of life."
More indepth reading of the research seems to indicate that nipple confusion is related to difficulty nursing or sucking in general.
As a speech language pathologist who works with infants having feeding difficulties, I believe that the infant is not confused. Rather, they are following the easiest option. Newborns have sucked, but never breathed before. Swallowing requires a complex pattern of suck swallow breathe. A pacifier allows sucking with minimal swallowing.
Weakness is another factor. The nipples of pacifiers, bottles, and mom's all require different motor skills to draw out liquid. The breast requires effort by the child. This effort builds strength and skills for later speech and feeding development.
If a child is struggling with breastfeeding, it is understandable that a nipple that produces no flow (pacifier) or one that controls the flow into the mouth (slow flow nipple) or quickly without effort (fast flow nipples) is preferred. These nipples do not cause the confusion, but rather reveal a difference or problem that is already present.
Some of these problems will likely show up later in slower development of feeding and speech skills.