When I clear all config off the Mikrotik it gives a warning saying it is dangerous. Is there really any danger? Is the danger that I might not be able to connect to it? That would make sense seeing the IPs are cleared but can use winbox. Is there any other danger?
IF connected to the internet and you add things in the wrong order, yes the possibility is there.
Yes, there is. The original configuration has one user (admin) and blank password. If your router is a SOHO model it comes with a firewall on the WAN port, that should keep you safe enough to create a new user, set a password and disable the admin user.
BUT
Switches (both CRS and CSS ones), and professional routers (CCRs and some others) come without firewall and without functions attributed to ports (WAN, LAN and so on). It is prudent to do the inicial basic config with the router offline, THEN put it on the internet.
OK, but no actual danger of locking yourself out or bricking it? I am studying the default config to see what they put in there by default, firewall rules etc. I just want to clear all config as a learning exercise.
You shouldn’t get locked out, just for removing ALL the configs. But You WILL loose the firewall. I don’t recommend this on a router connected to the internet.
It shouldn’t brick the router, just removing ALL configs. But You can always netinstall, if the worst happens. If You want to do some experiments, it would be a good idea to learn how to netinstall BEFORE.
I don’t know of any device in the world that when you reset to the default, lock out or is bricked…
For restore the default (complete clear)
/system reset-configuration keep-users=no no-defaults=yes
For restore the default and set basic firewall & dhcp
/system reset-configuration keep-users=no no-defaults=no
Thanks, that does make sense. I wouldn't have thought so myself but the warning said it was "dangerous" so it made me think twice. I was thinking more powerful devices (than your typical consumer router) might allow you to screw up in unforeseen ways. 
I really just want to learn to set it up without a default config so I know more what I am doing. I've had mikrotik for years but never really got to know them terribly well. Mainly because my internet relied on them so I couldn't play around too much, but now I have a spare
It is “dangerous” in the sense that you may lose a lot of work, and when you are connected in a way that relies on the existing config (e.g. a VPN) you may lock yourself out.
But when you make a backup (/export) before you reset it, and you make sure you can still connect locally (either via IP or via MAC), it is not dangerous.
Actually I just picked up an RB2011UiAS-2HnD-IN today. This seems to lock you out if you do a full clear config. The other one I have which is RB751U-2HnD you can clear config no worries.
EDIT: Actually I take that back. Removing the DHCP server would cause the PC to lose it's IP after a period of time which caused disconnection. I thought winbox was doing some magic where it didn't need an IP but clearly I was wrong about that.
Well actually winbox CAN do some magic where it does not need an IP!
When you have cleared the config and not loaded any defaults, the router will not have an IP but you can still connect it via the MAC address from a PC directly connected to the LAN port(s).
Then you can start the config from zero.
But in typical use as a NAT router it would not be advisable to do so. It is better to let the router load its default configuration, then connect the PC to a LAN port (i.e. not ether1 or sfp) and it will get a 192.168.88.x IP using DHCP and the router will be 192.168.88.1
Then work from that default config to make it as you require, i.e. set a password, configure the correct type of internet connection, etc.
Yes, that makes sense and I have done that before. What I meant though is the PC has to have an IP. For me it would not work when the PC got its 169.x.x.x self assigned address. I had to set a static IP to get it to work.
To summarize this thread: it is dangerous to clear config if one doesn’t know some networking basics and doesn’t have Winbox at hand. Otherwise clearing config is not dangerous, it won’t physically damage device or something.
Is that comment directed towards me?
If you are doing a layer 2 connection to the router via winbox, no IP address is needed on either the PC or the router. But..once you configure the router with an IP address on the WAN or any of the interfaces or bridges, you still use layer 2 connection or give yourself an IP on the same subnet and then access the router via winbox that way.
So what I was seeing is that when I removed the DHCP server config, after a period of time the PC would lose it’s IP and go back to the 169.x.x.x self assigned address. When it did that the connection would drop out and there was no way I could see the router at all in winbox. When I pushed refresh to scan for routers it would show nothing. This was with my laptop connected direct to the mikrotik via ethernet and wifi on the laptop turned off. Solution was to provide an IP on the PC, possibly any IP would have worked. I always connect via the mac, not the IP. This confused me a lot as this didn’t happen with my other mikrotik but it’s hard to remember the exact steps I used previously.
No, it’s a general remark. I don’t know your networking skills hence I can’t judge if clearing config is dangerous for you in particular.
My guess is that it’s dangerous for, say, 99% of Mikrotik owners and for 90% of forum members (I was included during the first month of my exposure to Mikrotik mainly due to second part of my sentence - the part you chose not to quote).
To summarize summarized quite rethorical question of OP: Is it safe to format disk and install on computer fresh instance of any OS?
Clearing the device is safe but connecting it to the net without checking/presetting some crucial information could led to a risk.
Do not expect full multipage story explaining all pros&cons be presented as a remark before pressing “Clear configuration?”.