Well, it might be "apartheid in football" if they were forming a black players only league or similar - are they? Do their articles of association propose only passing to other black players, or only tackling white player? No, they don't, so a hyperbolic question really.
Most of these bodies to which you refer ( rather like the society of black lawyers, and the national black police association) are formed to promote initiatives that reduce discrimination based around race/ colour, a discrimination that has been around for centuries. None of these organisations are promoting any kind of apartheid or anti-white agenda.
No question that Britain is far more equal and tolerant than it once was, and no question that it is probably the least racist country in europe - but that does not mean that all the battles are won, that discrimination has disappeared.
If some black players wish to form an association devoted to fighting racism because they feel the current measures and initiatives have stalled or become complacent, that is entirely up to them it seems to me.