There is a difference here.  Kaepernick's act is political protest; Tebows wasn't.  And yes, the fact that he's protesting inequality does make it okay.  Dropping to a knee and thanking Jesus for scoring a touchdown is, well, not wrong, but kind of tacky.  Look at me, America!  I'm a Christian! 
Protesting inequality is not disrespectful in America, or it shouldn't be.  The second paragraph of the Declaration of Independence says "All men are created equal...".  Aren't these athletes simply demanding that their nation live up to it principles?