Here's why you shouldn't care.

The rule that you could not make commercial use of Minecraft has existed for a long time, since December 11th of 2013 at least. Read the "One Major Rule" section. Has that ever stopped anybody from making ad revenue from Minecraft? No. Has anyone had their videos taken down yet for this reason? No.
While there is no guarantee that Microsoft will be more strict about this rule than Mojang was, we really shouldn't care until we find out for sure.

As for the rule that you can no longer mod the game, can you point me in the direction of where it says that in either Microsoft's or Minecraft's EULA? I'm having difficulty finding that. All I found in Microsoft's TOS is this:

What if I create something new in your universe?


Distribution of your Item in any form constitutes a grant by you of a royalty-free, non-exclusive, irrevocable, transferable, sub-licensable, worldwide, license to Microsoft and any of Microsoft's partners or users to use, modify and distribute that Item (and derivatives of that Item), and use your name if we choose to, for any purpose and without obligation to pay you anything, obtain your approval, or give you credit. And this license to Microsoft survives any termination or expiration of these Usage Rules. This means that if you add to the game universe or expand on the story told in the game with "lost chapters" or back story or anything like that, distribution of your story or idea may appear in a future game without any compensation to you. (Sorry, but our lawyers tell us we need to do this in order to avoid frivolous lawsuits getting in the way of making more great games.) It also means we can put your Item on a Microsoft site or property like Halo Waypoint if we want to.

Roughly translated to normal people language, this means that any modifications you make to a Microsoft game can be added to the real thing with no payment or credit to you. Cool. Lots of Minecraft mods are no longer necessary because Mojang added their functionality to the vanilla game. Did you see mod creators crying about not getting paid or not receiving credit from Mojang? No.

As a final point, this is the gaming industry. Look at what happened when Flappy Bird went down. Clones were popping up all over every market left and right. If Minecraft loses its following because of Microsoft's purchase of Mojang, someone will just make a different game with all, if not more of the same features.

TL;DR until you see Microsoft suing server owners and doing mass-takedowns of Youtube videos, for the love of all that is holy don't get your panties into a bunch. Microsoft isn't as evil as every gaming blog makes them out to be.

 

Phil Spencer on Twitter: "Minecraft YouTubers, you’re a great part of Minecraft’s success and we have no plans to change what you’re doing once we close the deal."