Jira won because it was not opinionated. You can use it however you want. FogBugz had the philosophy to make bug entry super easy above anything else. Jira will let a manager define new custom fields and make them all compulsory. It perfectly fits how manager at big companies think.
FogBugz provides Completion Date Probability Distribution chart and Burn Down Chart [2]. Anyone who has worked for big companies knows that these two are USELESS for them. They set a project delivery date and you just have to hit it.
At my current company, we are going for SOC1 compliance. This forces an amazingly complicated issue workflow and they implemented it very easily in Jira. I am looking at FogBugz documentation on workflows [1], and I don't see how we could have implemented the same in FogBugz.
I also feel that Jira has a better ecosystem for plugins and integrations then FogBugz.
[1] http://help.fogcreek.com/7483/statuses-categories-and-workfl...
[2] http://www.fogcreek.com/fogbugz/features/project-management/