I don't know if the NYT actually does publish more negative articles about Deutsche Bank than other banks. But if what you're perceiving matches reality, I would assume it is for the following two reasons:

1. Deutsche Bank facilitated a basket option trading strategy used by Renaissance Technologies, which has since earned the latter an investigation from the IRS for aggressive tax avoidance. RenTech is (unfortunately) synonymous with Robert Mercer's political activity in the eyes of many because he was a major partner and CEO of the hedge fund before he stepped down last year. This leads to my second point.

2. Deutsche Bank is (separately from RenTech) involved with Donald Trump in a number of real estate dealings, which other commenters have already cited. Regardless of your personal stance on the president, the NYT is going to spend time investigating any areas of financial misconduct it can find which may be directly or indirectly related to the president.