Players who register late are at a severe disadvantage because of their stack to blinds ratio. If you register early you should be happy that others register late because you will have an advantage over their stack, making it easier to accumulate chips.
This is actually quite a bit up for debate. According to ICM (Independent Chip Model), when some players bust, the value of each chip go up. This is why, you are generally happy about it, if two other players with stacks similar to your own end up in an all-in situation. Even you were not involved in the hand, your chance of cashing has just gone up, because now there is one less player, you need to outlast.
So in principle it is actually unfair, that some players are allowed to not enter the tournament and not pay the blinds and antes, until maybe half the field has already busted. These players also get an advantage in the sense, that they dont need to learn deep stacked play, because they can get right into the push or fold phase.
Now it could be argued, that they also dont gain the advantages, which it is to play with a big stack and push the other players around. And that is true. They also dont get as much time to use their skill edge, if they have any. But its still not a level playing field, when people enter at different stages, and therefore it would be fair to at least limit the time for late registration and in relation to this rebuy or reenter, when this is allowed.
For me personally I think, allowing late registration for the first 3 blinds levels would be a reasonable compromise. If people are any later than that, they just play the next tournament, which online is never far away.
But I am sure, this is not going to happen, because there is both tradition and money involved. For starters most tournaments have a quarantied price pool, and obviously poker sites want to give as many chances as possible for that number to be exceeded, so there is no overlay.