Comparison is a false analogy.
A false analogy is a fallcy that attempts to compare to things that don't warrant comparison. In this case, the term "separate" referred to physical-material segregation, whereas gay marriage refers to a social classification.
Relating to or affected by a policy whereby two groups may be segregated if they are given equal facilities and opportunities. For example, They've divided up the physical education budget so that the girls' teams are separate but equal to the boys. This idiom comes from a Louisiana law of 1890, upheld by the U.S. Supreme Court in Plessy v. Ferguson, "requiring all railway companies carrying passengers on their trains in this state, to provide equal but separate accommodations for the white and colored races." Subsequently it was widely used to separate African-Americans from the white population through a general policy of racial segregation. In 1954, in a unanimous ruling to end school segregation, the Supreme Court finally overturned the law (in Brown v. Board of Education).
Read more:
http://www.answers.com/topic/separate-but-equal#ixzz1Keg14Jix