I think what makes website ads different from YouTube ads is that the YouTube ones are directly linked to the artist and not much else. The only relevant part of OCReMix's YouTube uploads is the remix, which links the money directly to the artists. When the ad is on the website, it's harder to link the money to the artists and instead it feels like the money goes directly to the website.
I don't have a defined opinion about this (and only have 1 posted remix haha) but I can see why it would bother some people since this way it feels like your work is directly generating money while it didn't feel that way before.
Regarding the ads themselves, I recently listened to some of the newest remixes and didn't notice the ads. I probably had ad block though... Either way, if there are going to be ads in the videos, I feel they should be the ads that just show a message instead of those video ads that play before a video. The latter ones are obnoxious as hell.