Her writing on transgender issues has been criticized as transphobic; the University of Rhode Island released a statement distancing itself from her views, while recognizing her academic freedom.

Additionally, she has published research and analysis on the role of the Internet in facilitating sexual exploitation and trafficking of women and girls, and on the mail-order bride industry.

[14][15][16][17][18] Hughes suggested that government-funded HIV prevention programs should check that sex workers were not victims of abuse, rather than simply hand out condoms.

[22] In March 2021, Hughes published an essay titled, "Fantasy Worlds on the Political Right and Left: QAnon and Trans-Sex Beliefs", on the self-described radical feminist website 4W.

[23] The essay compared the beliefs of transgender activists to the right-wing conspiracy theory QAnon, and characterized various hormonal and surgical treatments and pro-trans language reforms as dystopian.

[4][23] Such statements prompted backlash from students and faculty at URI, who considered the essay transphobic and emblematic of larger problematic culture at the university.

[23] This response prompted the University of Rhode Island to release a statement distancing itself from the essay, while affirming Hughes' general academic freedom to express such views.

[24] From 2006 to 2009, Hughes was a leading figure in the campaign to end the decriminalized status of indoor prostitution in Rhode Island,[14][25][26] so that police could conduct anti-sex trafficking investigations.

[35] A March 2010 editorial in the Providence Journal claimed that Hughes has faced threatening remarks on various internet forums from patrons of massage parlors in retaliation for the role Citizens Against Trafficking played in the banning of indoor prostitution in Rhode Island.