While Bundy has a ranch of considerable acreage, since it's desert shrub (vs., say, grassland) in Nevada, it requires much more land to graze his 900 or so cows. And so, like other ranchers, he partly grazes his cattle on adjacent government land. In reports I've seen, there is dispute (and therefore uncertainty) about whether this land is either state or federal land.
The adjacent "government" land is not used for anything, and therefore it deprives no one for Bundy to graze his cattle there.

Beyond that:
1. The rent was not always charged. And the Bundy family has challenged the legitimacy of these fines in court for 20 years and ongoing. Although so far the courts have sided against their assertion that they shouldn't have to pay the fees.

2. In addition Bundy previously had 52 other cattle-ranching neighbors who have been driven off their land and forced to sell by these federal agencies. So while it's not officially called eminent domain, that's ultimately what it's about: driving these ranchers off their land so that the federal government (or federal defense contractors) can seize their land and use it for their own purposes. As this real estate broker attests to.

And ultimately, it's about Agenda 21, locking down authoritarian control on the country, and eliminating the potential for people to live independently in rural areas where they can provide their own food and protect themselves with guns, outside of urban areas, without dependency on government and mainstream food supplies.