Why does Johnny like it better when his father is hitting him?

As other answers have stated, Johnny prefers to be hit by his father than ignored wholesale by his parents, which seems to be the usual state of affairs. His terrible emotional neglect by his family highlights his sense of vulnerability. For him, the Greaser gang really does become a vital substitute for his own cold, uncaring family. He finds the love among the gang which is so markedly lacking for him elsewhere. In fact, he is described as being 'the gang's pet'.

Although the other Greasers might sometimes scrap amongst themselves, they won't ever do anything to Johnny. This is best illustrated in the incident when Dally is annoying Cherry, the pretty Soc girl, at the cinema, and Johnny intervenes and warns him to 'leave her alone'. Dally is thereby thwarted, but he can't retaliate against Johnny - although, as Ponyboy notes, if it had been any other Greaser, Dally wouldn't have hesitated to beat him. However, he can't lay a finger on Johnny, who holds a privileged position in the gang:

But Johnny was the gang's pet, and Dally just couldn't hit him.

Dally, in fact, appears to be closer to Johnny than to anyone else; and when Johnny dies near the end of the story, Dally is completely unable to cope.

The Greaser gang, then, becomes Johnny's substitute family. Ponyboy sometimes feels aggrieved at his own family life - the loss of his parents, his constant run-ins with Darry - but he comes to appreciate that he still does have the love of his brothers, whereas Johnny has absolutely no-one outside of the gang.