They ended up together as friends and family and loved ones, just not as lovers. Honestly, fans should probably just be happy that both of them lived to the end of the series, and they really did get happy endings.
Are Sherlock and Watson in love?
No, there wasn't. In fact, Arthur Conan Doyle specifically made Watson a man to make sure there was no chance of any romantic implications in Holmes's life. John Watson is quite clearly not a gay man. He has dated women all his life and married a woman called Mary Morstan.
Does Watson cheat on Mary?
John Watson : I cheated on you, Mary. There's a woman on the bus, and I had a plastic daisy in my hair. I'd been playing with Rosie, and this girl just smiled at me. That's all it was.