Does this say:

... that Moetzet YESHA is a "tool" of the government?

From what I understand of this article, the Moetzet YESHA demonstrations were "kosher" while all the others, the Bayit Le'umi and unaffiliated demonstrations were a form of "rebellion," not the pained voice of patriotic dissidents.

Read these paragraphs:

"The focus of the trial [against the Bayit Leumi] was to differentiate between protests," prosecutor Dan Bahat said. "The [Jerusalem Magistrates] court concluded that the aim of the [Bayit Leumi road-blocking] demonstration was not a protest but to foil a government policy. Sderot residents also blocked roads during their protest but their aim was to focus public attention to their plight. The aim of the respondents was to silence the state and to physically prevent the implementation of the Disengagement."
The three respondents -- Shai Malka, Adiel Sharabi and Ariel Vangrover deemed the leaders of the National Home [Bayit Leumi] movement -- were acquitted of sedition and incitement against the government for planning a mass road-blocking in May 2005.
Jerusalem Magistrates Court Judge Rachel Shalev-Gertal ruled on Sept. 2007 to acquit the three on the grounds of selective prosecution. The state prosecution appealed the decision.
"We are asking for the annulment of the selective prosecution [decision]. If there's a conviction, we want imprisonment," Bahat said on Feb. 12 at the Jerusalem District Court."
Bahat said the protest campaign was planned solely by the three defendants -- in contrast to Jewish settlement leaders who sought to avoid unrest*. Bahat said the highway shutdown plan, a method often used by Israeli labor unions, marked a revolt against the government. (*emphasis mine)

"Jewish settlement leaders" are the government paid/backed Motetzet YESHA

Now, this job of their was/is to "avoid unrest." That's a very interesting euphemism, isn't it? That's why the government-paid official rabbis have been working so hard to sedate their followers with talk of "G-d's will," etc.