I think some people have more testosterone, and can more easily raise their testosterone levels. I am talking about naturally, steroidal use is a whole separate topic. Of course, muscle is only one aspect of being an athlete. Some sports as mentioend above need precision hand eye coordination. Others need a great ability to know where your body is in the space you are in. Some take seemingly higher levels of adrenaline, while others need a lot of concentration and reduction in anxiety. Take football vs. golf. Football the players are revved up with energy from the loud crowd. Golf the player needs to calm down and have a lot of control and noise from the audience is frowned upon. Some sports are group efforts, some individual.
I doubt athletes have more Neanderthal genes. I would guess we all have some genes that trace back to that. I think our environmental situation influences what physical or mental attributes we emphasize and promote.