I don't know exactly what you meant by saying that "Felipe didn't like how his mom being treated by his father", but if we have to believe the rumours... Felipe inherited the same Borbón's tendencies as his father and his grandfather... So he wouldn't be the right one to criticize his father (at least, not anymore...)
AT THIS STAGE, I have no doubt that the F&L marriage is good & happy, they have two small daughters and are often labelled as "acccomplices" which I find is true judging from pictures. After all it was Felipe who wanted Letizia to share this enormous burden with her, why would he feel to annoy her at such an early stage?
BUT, I believe that, although they were less "in love", the marriage between JC and Sofia was similar at the beginning, both married in order to pursue a "project" (something that Letizia said of her future life with Felipe, too) and to share a professional aim, the claim of the Spanish throne. I believe they were "accomplices" too, Sofia was very important for JC, she was able to charm people, incl. General Franco, and to help the cause a great deal. The time was not for "lovey dovey", but I believe that their marriage was strong and good at this stage, there is a reason why JC later called her "the great professional".
F&L are only together for less than nine years and it is yet to be seen whether the burden of the position will make or break them. Pressure over decades will make people change, and I have no doubt that Felipe will change as King, personally and professionally, like his father did. Whether the ageing consort, not born into royal life, can keep up or is allowed to keep up or wants to keep up remains to be seen. There will be so many worries in their lives to come, about becoming Kings, remaining Kings, Leonor & Sofia becoming teens & adults with media pressure being unleashed on them (what I believe will be Letizia's horror), the parents having to let go and disagreements about their daughter's decisions, fading looks ... will they still be accomplices in decades to come? I wouldnt bet on it.
Sofia is who she is, Queen of Spain, what she enjoys, a born royal with a firm position and reputation within the royal community, and she probably couldnt care less for JCs antics at this stage. I am not sure Letizia would feel as secure as Sofia in the same position.
The real strain on the Kings' marriage started in the early 80ies - JCs philandering and doing his own thing in his Men's World - if I am correct and it only deepened with the children becoming adults, taking their own decisions that one parent might support, the other one doesnt. Today I believe the relation is completely strained, only the professional basis for the greater good has remained, JC has been rude in public towards his wife, and Sofia's biography was probably one of the last straws for JC.
And last but not least in terms of the Kings liking Letizia or not: I dont believe she was welcomed at Zarzuela, they tried to kill the relationship and only gave in when there was no other option. But with marriage and time passing, I am sure they got over it and these days will appreciate her for doing a professional job.
What I never fell for though was the friendly demeanour of the Queen towards Letizia, it is very "Sofia", something I called acting, others might call professional. While I do believe that their relation is friendly/professional, I never believed the "best friends/accomplice" stories for a second. Sofia will smile with anybody, even an unfavoured daughter in law, as long as it serves the purpose of keeping the Spanish throne.
