Equal rights haven't been afforded universally primarily because no one can agree who should get equal rights or what these rights should be. These days, in America, it's generally agreed that all sexes and races deserve equal rights1 and homosexuals and transsexuals are getting there, but the few people who want to grant suffrage to children, serial killers, and non-humans are considered by most to be—to say the least—extremist radicals.
Even once we decide who gets equal rights, we have to decide what they are. Freedom of speech? (Even directly encouraging violent crime) Freedom of religion? (Even Human sacrifice?) Some people want just negative rights, others want a massive amount of positive rights to the extent of creating a massive welfare state.
Many nations have made great strides towards equal rights in the past several hundred years, but even oppressed groups have sometimes resisted new measures. The Equal Rights Amendment, for example, was opposed by many women because they felt it was a threat to family values.
Although attempts to increase equality generally target women and minorities—due to their being the most discriminated against—there have been cases in which the legislation has been to benefit others, such as in Craig v. Boren where the court decided that it's illegal to have the legal drinking age for females lower than for males.
Some of the most significant moves to increase equality in the U.S. are the 1964 Civil Rights Act, the decisions in Brown vs. Board of Education, the end of slavery and ratification of Amendment XV following the Civil War, the Voting Rights Act of 1965, the creation of Amendment XIX, and the findings of Romer v. Evans.
1 Note that this writeup is from before September 11, 2001. Last I heard, over 40% of Americans supported restricting the civil liberties of Arabs in particular. | 
