She was very powerful in the sense that she was extremely wealthy, in fact, she was the third biggest landowner in Royal Hungary. Politically she was also well connected, but as it turned out, she was connected to the wrong people.

As I don't know much about her in particular, I will introduce the historical background, maybe that will help to assess her situation for yourself. As I have other very urgent tasks I should be doing, I will be extremely verbose so I can put those tasks off for a while.

Ever since 1526 Hungary was mostly only a step or two away from civil war. There were two main parties, one for the national kingdom, as in having a Hungarian king, and the other party favoured the personal union with Austria and Bohemia through the Habsburgs. The next ten years after Mohács were spent in a bloody and incessant civil war, while the Ottomans showed up for good measure every two or three years to kick in the teeth of whoever was willing to oppose them. Nominally Szapolyai János, the Hungarian king candidate was an ally/vassal/minion of Suleiman the Magnificent, but the Turks either kept very bad discipline or didn't feel like enforcing it in Hungarian territory, because they were burning and pillaging as badly as back when they were still enemies.

Finally, in 1538 a peace agreement was brokered between the two sides. Habsburg Ferdinand recognised Szapolyai János as the king of Hungary, in exchange of Ferdinand becoming his heir. János agreed, as he had no son. Then his wife bore a son, I. János kicked the bucket, and civil war round two commenced.

The end result this time, was that Northern and Western Hungary became Habsburg territory, II. János held Eastern Hungary, while the Ottomans were fed up with all this vassal state and puppet kings bullshit, and directly occupied the Central and Southern counties of Hungary, taking a few forts every year when they could spare a big enough army.

Finally a new peace was brokered in 1570, II. János abdicated in favour of the Habsburg king Maximilian, and swore fealty to him. In exchange he became the prince of Transylvania and the Partium, something very similar to an imperial prince in the HRE. Thus order was restored, and now that the country's two most powerful parties came to an agreement finally they could start to kick the Ottomans off the lawn, and...

No, of course that's not what happened. II. János kicked the bucket without an heir in 1571, and the whole "finish the half century long civil war" plan went to hell. You see, the Ottomans didn't particularly like the idea of Hungarians stopping killing each other and focusing on kicking them out, and they insisted that the Transylvanian diet not recognise Maximilian as the ruler of Transylvania and the Partium. Or else.

Meanwhile Maximilian, according to the treaty of Speyer was now rightfully Transylvanian prince and Hungarian king as well. And the Transylvanian diet better recognise him as such. Or else.

After brief consideration the Transylvanian diet decided that the Ottomans had a bigger and scarier army, and elected Báthory István, the suggested candidate of the Sublime Porte. Cue civil war round three.

Báthory István in the end proved to be a very capable monarch, he even became Polish king, and a damned good one. But the chance of reuniting the country slipped further with every passing year.

To say the least the next three decades were confusing. Not as confusing as the War of the League of Cambrai, but close enough. Plenty of civil wars, abdications, normal wars, renouncement of abdications, occupations, changing sides, and some more civil wars for good measure. From the rubble emerged a Transylvanian Principality that would not even hear from recognising the Habsburgs as rulers of Transylvania, and a Royal Hungary that was not very fond of its Habsburg rulers, and all told, found the Transylvanian idea of a Hungarian king quite appealing. In 1605 the Transylvanian prince, Bocskai István went through the whole of Royal Hungary, and forts overall opened their gates for him, while Protestant nobles joined him, swelling his armies. Bocskai soon died, temporary peace resumed, but in 1608 a Báthory was elected again, this time Báthory Gábor, a cousin of Báthori Erzsébet.

So Báthori Erzsébet was not just wealthy, but well-connected. She wasn't terribly interested in politics, as far as we know she spent her time managing her estates and raising her children, but her relatives and friends happened to be politically very active.

Her now dead husband was a leader of the opposition in the diet of Royal Hungary. Bocskai István was an old friend of hers through her husband. And now her close relative was prince of Transylvania, probably hatching evil plots to take over Royal Hungary. Well, that last one was actually true, but nothing ever became of these plans.

Anyways, the palatine of royal Hungary, Thurzó György was a tiny bit paranoid after all these civil wars. As the highest official of Royal Hungary, and a good friend of King Matthias II, he did not see the appeal of Transylvanians occupying Royal Hungary yet again. So he acted to remove the enemy's potential fifth column. And also maybe to take a few bites here and there from those big juicy estates while no one was looking.

Either that, or Báthori Erzsébet was really a witch bathing in blood of servant girls. Though as far as I know, most of the testimonies against her were made under torture, so that seems unlikely.