I agree jQuery was very useful early on, especially since it abstracted cross-browser differences and APIs.
However in my experience, a couple of things were key to creating a negative view of jQuery:
1. Security and unsafe defaults, for example: evaluating remote JavaScript by default [1]; and unsafe DOM parsing by default [2]
2. Not really to blame on jQuery, but its ease of use for DOM manipulation led to programming patterns that aren't easily scalable, for both code and performance
[1] https://nvd.nist.gov/vuln/detail/CVE-2015-9251 [2] http://api.jquery.com/jQuery.parseHTML/