You could put a good Ness against say a same level

and the Ness still has a perfectly good chance of wining because of how he is played as well as used to his full potential.
Ness' full potential is much (emphasis on "much") lower than Fox's. At low levels character strength/potential isn't really relevant, because low-level players aren't capable of using the things that make the good characters good (so in a sense all characters are equally bad when played by bad players). At high levels, the Fox players can use Fox's strengths to gain advantages, while the Ness players cannot use Ness' strengths to the same extent, because Ness simply does not possess them. Ness' chances of winning against Fox in a game between two equally skilled players reduce as the level of play increases.
It might help to think of it like this:
• A character has a "level" between 0 and 100; Fox has a level of 100, and Ness has a level of 20 (because Fox is the best character while Ness is one of the worst).
• A player has a corresponding level, also between 0 and 100. Imagine 2 players, Player A with a level of 100, and Player B with a level of 20.
• The effective strength of a character/player cannot exceed the lowest level of the character/player
• Even if Ness is used to his full potential by Player A, Ness is only good enough to hit 20 even though the player has the potential to perform at level 100. Therefore the performance from Player A using Ness will be at level 20.
• Likewise, even when using a character with a level of 100 (Fox), Player B lacks the skill to play better than level 20 even if the character gives them the opportunity to go up to 100. Therefore the performance from Player B using Fox will be at level 20.
• Ness will never exceed level 20 even with the most skilled players, while Fox can reach level 100 with the most skilled players.
• A game between a level 20 Ness player and a level 20 Fox player will appear even, while a game between a level 50 Ness and a level 50 Fox will favour the Fox. A game between a level 100 Ness and a level 100 Fox is practically unwinnable for the Ness player. The Ness player is still stuck at level 20 while the Fox isn't limited to the same extent.
People aren't "missing the point" when using a tier list; they acknowledge that bad characters can do well in the right hands, it's just that good characters can do even better. At top levels, good characters do so much better than bad characters that there's practically no way that the bad characters can win. This is why you never see, say, Pichu winning tournaments; it's not that Pichu's meta is underdeveloped so much as that even if Pichu was as optimised as the top tier characters, they would still stand no chance of winning because an optimised Pichu is drastically weaker than an optimised Fox/Falco/Marth/good character. Tiers exist, and in a game as badly balanced as Melee, they matter a lot.
This article is relevant:
http://www.ssbwiki.com/User:Semicolon/Treatise_on_the_Existence_of_Tiers