Here is the essential difference: everyone acknowledges that Israel is the Sovereign Power in the Negev, ergo, if it wants to use eminent domain to push the Bedouin's around then that's an issue under ISRAELI law, and is therefore an argument between (a) the state and (b) some of its citizens. But Israel is not the sovereign in the West Bank, so it's attempts to confiscate foreign land for the use of its own citizens is a violation of INTERNATIONAL law. And that's everyone's concern, which is why everyone complains about it.
Report: Palestinian, 18, killed in clashes with IDF in West Bank (Haaretz)
from the article: A double standard on disputed land for settlers and Bedouin