The statement of Rambam in question, is Hilkhot Mamrim (6:1)
כיבוד אב ואם מצות עשה גדולה, וכן מורא אב ואם--שקלם הכתוב בכבודו ובמוראו: כתוב "כבד את אביך, ואת אימך" (שמות כ,יא; דברים ה,טו), וכתוב "כבד את ה', מהונך" (משלי ג,ט); ובאביו ואימו כתוב "איש אימו ואביו תיראו" (ויקרא יט,ג), וכתוב "את ה' אלוהיך תירא" (דברים ו,יג; דברים י,כ). כדרך שציווה על כבוד שמו הגדול ומוראו, כך ציווה על כבודם ומוראם
Respecting one's father and mother is a great positive commandment, and also revering one's father and mother--Scripture equated them to His respect and reverence. It is written: "respect your father and your mother" and it is written: "respect God with your wealth". And [similarly] regarding one's father and mother it is written: "A man should fear his father and mother" and it is written: "You shall fear your God your Lord". In the same manner that He instructed regarding respecting his great name, and its reverence, so too did he instruct regarding their honour and reverence.
As you can see, Rambam is discussing the importance of honouring one's parents, and God, respectively. He says absolutely nothing about there being any causal link between the former and the latter.
Accordingly, there is absolutely no question of why according to Rambam, someone possessing the former, might nonetheless lack the latter.