Emacs's default keybinds are of some infamy, and RSI memes abound aplenty.
The simple fact is that they are not very ergonomic, at least not for modern keyboard layouts.

Luckily there's a few ways to remedy this situation.

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1. Ignore the issue entirely and pretend everything is okay

Alternatively, get yourself some foot pedals...
https://www.emacswiki.org/emacs/FootSwitches

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2. Remap Ctrl to another button

There were keyboards designed for writing lisp: https://upload.wikimedia.org/wikipedia/commons/4/47/Space-cadet.jpg
You'll notice that Ctrl, the most commonly used modifier key is also the closest to the spacebar.
This means you can easily hit Ctrl with your thumb, instead of modern keyboards where you'll be straining to stretch your pinky to hit it.

Swapping Alt and Ctrl is common.
As is swapping Ctrl and Caps Lock (though it has some issues http://ergoemacs.org/emacs/swap_CapsLock_Ctrl.html).
You can do this at the OS level with xmodmap, or internally in emacs if you don't want to fuck up your other keybinds.

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Globally via setxkbmap:
setxkbmap -option ctrl:swapcaps
or
setxkbmap -option ctrl:swap_lalt_lctl

You may also want to have Caps Lock as Ctrl and Ctrl as Hyper key (Hyper key can be used for shortcuts, "H-n" means "Hyper+n"):
setxkbmap -option ctrl:swapcaps_hyper

More information: man setxkbmap and man xkeyboard-config
Note: you probably want to auto-execute this when your X session starts

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Globally via X.Org configuration file:
1. Create and edit /etc/X11/xorg.conf.d/00-keyboard.conf
2. Paste the following:

Section "InputClass"
        Identifier "system-keyboard"
        MatchIsKeyboard "on"
        Option "XkbOptions" "swapcaps"
EndSection

2.1 Put your own setxkbmap option instead of "swapcaps" on line 4 if you need it.
3. Restart X.Org or reboot.

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Globally via an xmodmap file:
Save as ~/.Xmodmap

! Swap Ctrl and Alt
clear control
clear mod1
keycode 37 = Alt_L Meta_L
keycode 105 = Alt_R Meta_R
keycode 64 = Control_L
keycode 108 = Control_R
add control = Control_L Control_R
add mod1 = Alt_L Meta_L

or

! Swap Ctrl and Capslock
remove Lock = Caps_Lock
remove Control = Control_L
keysym Control_L = Caps_Lock
keysym Caps_Lock = Control_L
add Lock = Caps_Lock
add Control = Control_L

Then run `xmodmap ~/.Xmodmap`
Note: you probably want to auto-execute this when your X session starts

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In Emacs only:
;; Swap Ctrl and Alt
;; V26+, X11 only
(setq x-ctrl-keysym 'meta)
(setq x-meta-keysym 'ctrl)

Note that many terminal binds are the same as emacs, so doing it only in emacs  as opposed to globally would lead to inconsistency.
For more info see https://www.gnu.org/software/emacs/manual/html_node/elisp/X11-Keysyms.html

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3. Use an external package

evil-mode: Probably the most common, as vim keys are pretty widespread and many migrants to emacs are already used to them.
evil-collection and evil-escape are also nice mentions, as they make the vim experience a lot more consistent.
The downside of course is that you're removing the "emacs"ness of keybinds, many prefer to stay more vanilla.

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god-mode: Unlike evil, this keeps all of emacs's keys intact, you simple map a GOD-KEY to type commands more easily.
You simply hit your configured key, then every key you hit afterwards has C- prefixed to it.
SPC- lets you remove C-.
So  <C-x> <C-f> becomes GOD-KEY x f
And <C-x> b     becomes GOD-KEY x SPC b

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xah-fly-keys: For the more adventurous, following neither emacs defaults nor vim, it maps keys on a usage based scheme.
see for more info: http://ergoemacs.org/misc/ergoemacs_vi_mode.html

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Different typing technique: press Ctrl key with your palm, next to the base of your finger. Use modifiers on both sides of the keyboard (one hand shouldn't type a key and hold down a modifier at the same time) if it feels awkward.
Note: this is not possible on low profile, flat keyboards that you'll find on laptops and some rubber dome keyboards such as Logitech K810.

OR

Use both Ctrl keys and use your ring/middle/index fingers instead of the pinky.

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Sticky keys via xkbset. The advantage to this is that you don't have to hold down a key.
xkbset sticky -twokey latchlock ## set sticky keys, don't disable via twokey

More info in the man pages.
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Other links:

https://www.emacswiki.org/emacs/MovingTheCtrlKey
https://www.emacswiki.org/emacs/RepeatedStrainInjury