LOL! I don't think it's a big deal if people see it differently - sometimes we just want different things from fics/pairings.
For me, this one is a no brainer - sometimes I have to think about it more but instinctively this is what feels right to me with this pairing.
I do see Holmes as the sub pretty much in everything I've seen with him in it - the movies for example - Jude Law's Watson is SO the sensible one bringing RDJ's insane but genius Holmes down to earth. (I don't like those movies much though).
With Sherlock, it's John's grounding compared to Sherlock's semi-autism. It's in Sherlock pacing around between cases wanting to smoke and John being the one who tells him 'no' and Sherlock accepting that. It's John telling Sherlock to accept gifts graciously, and apologise when he's been rude etc etc. It's the fact that while Sherlock is undeniably in charge out in the field on a case, it's John who is more in charge in their domestic/personal lives because he has emotional intelligence and Sherlock is far more cerebral.
I also don't see what the point is of topping John in a way - I don't think subbing is about letting go of sadness and being alone although one could write a story that brought out those elements. Sherlock needs a break from the big brain for sure, and John is a very grounded person who can give him time out. Sherlock also needs someone to defer to because John is the ONLY person he does defer to. Sherlock might know a great deal but in the emotional arena he almost knows NOTHING - he requires a guide to normal, human, everyday experiences and emotions and John is that for him.
I think one also needs to see Sherlock's vulnerabilities and John's strengths as well. Sherlock had a bad time at school and is as alone as John - more so in many ways because nobody LIKES him. Lots of people like John, even if he's cautious about letting them in. Sherlock's lack of friendships do bother him - you see he was laughed at at school - in the Blind Banker, he introduces John as his 'friend'. John, not wanting people to think they're a gay couple, amends that to 'colleague' - and Sherlock's reaction is quite sad and upset about that - it's all minute nuances.
I also think Sherlock really needs bringing down. John doesn't - he's already very grounded. What would subbing do for him? He doesn't need escape, or to fly, or to be brought down, or to stop from self destructing. He doesn't look to me like someone who would enjoy pain, or bondage, or power play, or giving up control in order to get release. If we just want to take care of him then I don't think it needs a BDSM relationship for that - it'd work better in a normal slash relationship. I don't see him as someone who does need taking care of though - I think his thing is that he wants to take care of others - he's a doctor after all, and part of what he does for Sherlock is care taking - making sure there's food in the fridge, looking out for him, worrying about him, killing people who are a threat to him - etc etc.
Of course, this is all pie in the sky in many ways - a person can be entirely different sexually to how they come over in their real life! LOL! So I don't think it's something we should get unduly hung up on. I just think Sherlock comes into that category where fandom mistakes his bossiness and cleverness for dom-like qualities whereas in many ways I think they're the antithesis. it's surface domliness - about being smart, apparently self assured and ordering people around. Rodney suffered a lot from that too and he was utterly a sub in my view - although John Sheppard was less of an obvious dom to my mind. Gibbs and Tony are easily the least confusing dom/sub couple out there! LOL! Gibbs IS bossy in the field and has rank and age on his side, but he's also very grounded. He also likes to take his toppiness everywhere - not just in the workplace - it's in every aspect of his life. And of course we see Tony loving that and responding to it in a very submissive manner - but only with Gibbs. Tony's subbiness is very specific to one person whereas Gibbs's toppiness is all pervading <g>.
But Sherlock is naughty - he pisses people off, sometimes deliberately, to the point where he gets sent to prison briefly for it despite John telling him NOT TO DO IT. John gets to comment on and correct Sherlock's behaviour - Sherlock never does that with John. John is there to reel Sherlock in and try to stop him from his own worst impulses. He humanises Sherlock. Even without the BDSM, that's a point that was brought out by the show's writers very early on. That Sherlock without John has the potential to go bad - he acts out of hubris and he acts out of his belief in his own mental capacity without thinking about any emotional consequences. That's what John is there for - to temper that. In that way I don't see them as much different from Walter and Fox - Fox is brilliant but wayward - Walter is stabilising. I think people are maybe confused by the fact that John is the junior partner, ostensibly, in their working relationship. I also think some folks just love Sherlock and want to imagine him being the stern fantasy dom of their dreams. Nothing wrong with any of that - if that's how people want it. It really doesn't work for me that way but all of this is fantasy anyway.