TheCowWentMoo,
No reason at all that his Dad shouldn't have been the one to give up work to look after him, or that Tom should consider that second best to Gemma doing so. Pretty unremarkable for a child these days.
But as a teen already pissed off that your Mother's dating your teacher (so finding time for him outside her long working hours), whilst giving mixed messages to you about your Dad and simultaneously being back shagging him [and the horrors of hearing rough sex as evidence of it 
], Gemma's the handy one to lash out at for anything/everything. And far from blameless, tbh.
Not to mention the strain of Anna, his only confidante, leaving/ Isabel incident/ fight with best mate/ school grief etc. has got him so stressed he's seeing Dr Sian. He's not exactly thinking straight, so logic and fairness are out.
Expect would seem all the more raw, having witnessed your toddler half-sister doted upon, whilst your manipulative Father tells you that, by contrast, your Mother had made it clear she wished she'd never had you, slyly forgetting the bit about those being only temporary feelings whilst very ill, and likely has secretly felt that way ever since.
(I'm surprised he didn't also plant some lingering doubts in Tom's mind about whether Gemma had speeded up Grandma's demise ...).
Agree with you, though, a heck of a lot has been frustrating. We need a MN Q&A with Mike Bartlett.