What rights do students in the U.S. have re gender pronouns?
I think another answer here is misleading, so I am writing to clarify what federally protected rights transgender students in the U.S. can reasonably expect at this time.

As things currently stand:


The federal government is not allowed to pursue Title IX investigations that interpret Title IX's sex discrimination prohibition to include discrimination based on gender identity.
The Department of Justice and Department of Education have rescinded guidance (issued by the previous administration) that instructed schools to treat discrimination based on gender identity as a Title IX issue.
The U.S. Supreme Court may indicate later this year whether Title IX protections apply to transgender students who face discrimination based on gender identity. 




Previous federal guidance in the Dear Colleague letter of May 2016 considered discrimination based on gender identity to be sex-based discrimination. According to this interpretation, Title IX protections would then apply to transgender students who are subject to discrimination because of their gender identity.  This would certainly not have required school employees to use gender-neutral language as a general rule, but that letter did support e.g. 


a student's right to ask school employees and contractors to use pronouns consistent with their gender identity, 
the school's Title IX responsibility to mitigate (to the degree that they can) the harassment of students due to gender identity. There is legal precedent (see footnote 9 in the document linked above) to suggest that persistent misgendering can be considered sex-based harassment if it is severe or pervasive: "Persistent failure to use the employee’s correct name and pronoun may constitute unlawful, sex-based harassment if such conduct is either severe or pervasive enough to create a hostile work environment"


However, this interpretation - that Title IX protections apply to gender identity - was challenged in the courts in Texas v United States. An August 2016 injunction bars the federal government from enforcing the interpretation of Title IX put forth in the Dear Colleague letter:


  Defendants are enjoined from enforcing the Guidelines against Plaintiffs and their respective schools, school boards, and other public, educationally-based institutions. Further, while this injunction remains in place, Defendants are enjoined from initiating, continuing, or concluding any investigation based on Defendants’ interpretation that the definition of sex includes gender identity in Title IX’s prohibition against discrimination on the basis of sex.


The U.S. Department of Justice indicated an intent to appeal that Texas decision, and in November 2016, asked for a partial stay on the injunction, arguing that the injunction should only apply to the states involved in the lawsuit. A hearing on that motion for a partial stay would have taken place in February 2017. However, the new administration's Department of Justice withdrew that motion just before the scheduled hearing, noting that the "parties are currently considering how best to proceed in this appeal."  Shortly afterwards, the Department of Justice and Department of Education issued a new Dear Colleague letter withdrawing the guidance in the May 2016 letter.

Meanwhile, in March 2017 the U.S. Supreme Court will hear a related case, in which they may decide whether Title IX protections apply to gender identity. This case, too, is complicated by the withdrawal of the May 2016 letter, a move that has been communicated to the court.