% cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=16.04
DISTRIB_CODENAME=xenial
DISTRIB_DESCRIPTION="Ubuntu 16.04.1 LTS"

% dpkg -l | grep linux-im | cut -c 1-80
ii  linux-image-4.4.0-31-generic                4.4.0-31.50
ii  linux-image-4.4.0-34-generic                4.4.0-34.53
ii  linux-image-4.4.0-36-generic                4.4.0-36.55
ii  linux-image-4.4.0-38-generic                4.4.0-38.57
ii  linux-image-4.4.0-42-generic                4.4.0-42.62
ii  linux-image-4.4.0-43-generic                4.4.0-43.63
ii  linux-image-4.4.0-45-generic                4.4.0-45.66
ii  linux-image-extra-4.4.0-43-generic          4.4.0-43.63
ii  linux-image-extra-4.4.0-45-generic          4.4.0-45.66
ii  linux-image-generic                         4.4.0.45.48

% ls -1 /boot/vmlinuz-*
/boot/vmlinuz-4.4.0-31-generic
/boot/vmlinuz-4.4.0-34-generic
/boot/vmlinuz-4.4.0-36-generic
/boot/vmlinuz-4.4.0-38-generic
/boot/vmlinuz-4.4.0-42-generic
/boot/vmlinuz-4.4.0-43-generic
/boot/vmlinuz-4.4.0-45-generic

% uname -r
4.4.0-43-generic

% cat /etc/apt/apt.conf.d/01autoremove-kernels
// DO NOT EDIT! File autogenerated by /etc/kernel/postinst.d/apt-auto-removal
APT::NeverAutoRemove
{
   "^linux-image-4\.4\.0-43-generic$";
   "^linux-image-4\.4\.0-45-generic$";
   "^linux-headers-4\.4\.0-43-generic$";
   "^linux-headers-4\.4\.0-45-generic$";
   "^linux-image-extra-4\.4\.0-43-generic$";
   "^linux-image-extra-4\.4\.0-45-generic$";
   "^linux-signed-image-4\.4\.0-43-generic$";
   "^linux-signed-image-4\.4\.0-45-generic$";
   "^kfreebsd-image-4\.4\.0-43-generic$";
   "^kfreebsd-image-4\.4\.0-45-generic$";
   "^kfreebsd-headers-4\.4\.0-43-generic$";
   "^kfreebsd-headers-4\.4\.0-45-generic$";
   "^gnumach-image-4\.4\.0-43-generic$";
   "^gnumach-image-4\.4\.0-45-generic$";
   "^.*-modules-4\.4\.0-43-generic$";
   "^.*-modules-4\.4\.0-45-generic$";
   "^.*-kernel-4\.4\.0-43-generic$";
   "^.*-kernel-4\.4\.0-45-generic$";
   "^linux-backports-modules-.*-4\.4\.0-43-generic$";
   "^linux-backports-modules-.*-4\.4\.0-45-generic$";
   "^linux-tools-4\.4\.0-43-generic$";
   "^linux-tools-4\.4\.0-45-generic$";
};
/* Debug information:
# dpkg list:
ii  linux-image-4.4.0-31-generic                4.4.0-31.50                                amd64        Linux kernel image for version 4.4.0 on 64 bit x86 SMP
ii  linux-image-4.4.0-34-generic                4.4.0-34.53                                amd64        Linux kernel image for version 4.4.0 on 64 bit x86 SMP
ii  linux-image-4.4.0-36-generic                4.4.0-36.55                                amd64        Linux kernel image for version 4.4.0 on 64 bit x86 SMP
ii  linux-image-4.4.0-38-generic                4.4.0-38.57                                amd64        Linux kernel image for version 4.4.0 on 64 bit x86 SMP
ii  linux-image-4.4.0-42-generic                4.4.0-42.62                                amd64        Linux kernel image for version 4.4.0 on 64 bit x86 SMP
ii  linux-image-4.4.0-43-generic                4.4.0-43.63                                amd64        Linux kernel image for version 4.4.0 on 64 bit x86 SMP
ii  linux-image-4.4.0-45-generic                4.4.0-45.66                                amd64        Linux kernel image for version 4.4.0 on 64 bit x86 SMP
ii  linux-image-extra-4.4.0-43-generic          4.4.0-43.63                                amd64        Linux kernel extra modules for version 4.4.0 on 64 bit x86 SMP
iF  linux-image-extra-4.4.0-45-generic          4.4.0-45.66                                amd64        Linux kernel extra modules for version 4.4.0 on 64 bit x86 SMP
iU  linux-image-generic                         4.4.0.45.48                                amd64        Generic Linux kernel image
# list of installed kernel packages:
4.4.0-31-generic 4.4.0-31.50
4.4.0-34-generic 4.4.0-34.53
4.4.0-36-generic 4.4.0-36.55
4.4.0-38-generic 4.4.0-38.57
4.4.0-42-generic 4.4.0-42.62
4.4.0-43-generic 4.4.0-43.63
4.4.0-45-generic 4.4.0-45.66
# list of different kernel versions:
4.4.0-45.66
4.4.0-43.63
4.4.0-42.62
4.4.0-38.57
4.4.0-36.55
4.4.0-34.53
4.4.0-31.50
# Installing kernel: 4.4.0-45.66 (4.4.0-45-generic)
# Running kernel: 4.4.0-43.63 (4.4.0-43-generic)
# Last kernel: 4.4.0-45.66
# Previous kernel: 4.4.0-43.63
# Kernel versions list to keep:
4.4.0-43.63
4.4.0-45.66
# Kernel packages (version part) to protect:
4\.4\.0-43-generic
4\.4\.0-45-generic
*/


% apt-get autoremove
Reading package lists... Done
Building dependency tree
Reading state information... Done
0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded.

Why is apt-get keeping 5 old kernels although /etc/apt/apt.conf.d/01autoremove-kernels only protects 2 kernels?