This actually was a relatively simple answer; Franz Ferdinand despised Hungarians because they represented the one group in the Empire that undermined the Austrian nationalities control. And also were quite violent about defending their Sphere of influence in the Empire against anyone from the German portion. Let's provide some examples.

#1: Franz was a big enthusiast for the Federalist ideology within the Empire. These were individuals that supported granting more influence within the Empire to all states. Although this ideal existed prior to the 1867 compromise. It was afterwards considered a plan to finish the idea encapsulated in 1867. Hungary however was quite content with the current arrangement as particularly incorporating the Czechs (Who were much more industrialized) would threaten the balance of power; especially over Slovakia which was considered a realm within Hungary but in the past was traded in influence between the Czechs and Hungarians.

#2: Hungary was extremely unenthusiastic to the military ventures Franz Ferdinand wanted to undertake. Franz was for the lack of a better word, an enthusiast for the Austro - Hungarian navy and the international clout that it brought. He was a heavy proponent of sea power and was extremely alarmed when Austria-Hungary refused to deploy soldiers in the boxer rebellion when: "dwarf states like Belgium and Portugal" did so at a whim. This was a stance contrary to the Hungarian parliament, who wanted little to nothing to do with the integrated and jointly ran navy as it was out of their direct control. He also advocated for military and foreign positions that went against Hungarian aims. For example: He was cautious towards any hostile interactions with Serbia which was Hungary's #1 priority target at the time. He also wanted autonomy for the Croats, Slovenes and Bosnians under a third realm that would counterbalance the Hungarians. But these aims and that of a better equipped and funded joint army were frustrated in all of these by the Hungarian parliament.

#3: His biggest priority was ensuring the longevity and domination of his family over Austria - Hungary. The biggest problem with the Hungarian parliament to Franz was the fact it opposed many Austrian ventures. The Austrian parliament was for all intents and purposes still driven by the priorities and aims of the Hapsburg family. Therefore; Hungarian resistance to these often came at the expense of the Hapsburg dynasty rather than the Austrian government.