... the real challenge is civil rights protections for gays, lesbians, bisexuals, and transgenders.
The United States has no federal law spelling out that the protections of the 14th Amendment apply to lgbts. What few legal protections there are against discrimination in employment, housing, and public services for lgbts are a patchwork of local and state laws. Those few laws are vulnerable to being rolled back by popular referendum or by so-called "religious liberty" laws on the state level which make it a legal offense for cities and towns to enforce their own anti-discrimination ordinances.
The President can't really do much about marriage apart from public statements, but he can do something about this.