The issue is that Trample was designed to be a melee attack, but was determined to be overpowered when allowed to utilize all the different effects that interact with melee attacks. So, it was made into it's own category, but that meant it no longer had a complete framework to function off of. You are right that a lot of things, like flying and elusive, do not apply to trample if you go by the rules as written, simply because they don't make any mention of trample at all. But they definitely weren't intended to work that way.
In general, I'd say to treat it like a melee attack when it is detrimental to the Trampler, and not like a melee attack if it'd be beneficial. That probably isn't going to give you the intended result 100% of the time, but breaking it down on a case by case basis is a task that I'm not up to. Not as in that I'm unwilling to, but that I'm positive I'd get it wrong. It's just too big. Nobody would be able to tell you with certainty how to do Trample right in every situation until it gets errata'd.
But since the whole reason it is not considered a melee attack is to nerf it and keep it from being too powerful, I think that treating it always like a detriment and never like a benefit will have you handling it properly more often than not.
So....by that rule of thumb: You do have to lose flying when trampling, because that subjects you to dangers like counterstrikes. You can not ignore guards while trampling, because elusive applies to nimble melee attacks and not brute force charges.
