Nike trainers are perceived as being bad for a couple of reasons.
Nike does poorly in specialty running stores. Many running specialty stores simply don't carry Nike, period. Others don't push it very hard (Nike has been a notoriously bad partner for specialty stores). People who are into running (Runners World readers, not Letsrun readers) put a lot of stock in what they hear at specialty running stores. They see Brooks as the king of the big brands. They're also increasingly interested in boutique brands like On or Hoka. (Specialty running stores like the boutique brands as well because they don't get undercut by big box stores; On, in particular, is the least marked-down brand in the U.S. at the moment.)
Also, historically, Nike did not make very good "stability shoes" with medial posts. These types of shoes are popular with the average joe runner who is middle aged, carrying a few extra pounds, and has knee pain. It was probably intentional on Nike's part that it never courted this market segment. Nike would rather be perceived as a brand for the young and the fast, so it focused more on racing shoes and performance trainers.
Nike has not maintained a consistent and comprehensive lineup of training shoes. Shoes get frequently introduced and discontinued. While there are a couple of shoes that ostensibly are always in production, they frequently get totally reinvented. Moreover, this core line of shoes is pretty small compared to other companies' lines. This means that there's a good chance that in a given year, Nike won't make anything that you like, or if they do, you won't know what it is.
One thing that has helped Nike is that even though we're past the peak of the minimalism movement, one result of minimalism is that medially posted stability shoes are now a much smaller market segment. Lighter and lower drop shoes are more prevalent, and more running store associates are defaulting towards putting people in less shoe. A lot more people are looking at shoes like the Pegasus, which used to be seen as a shoe that was just for fast guys with efficient strides.