Original oneliner

ip link set arp off dev eth0 ; ip link set arp on dev eth0

Be sure to do it all at once, so you don't break network connectivity before you're able to turn ARP back on.

Interface discovering copy-paste command

interfaces=$(
  arp -n | awk '
    NR == 1 {next}
    {interfaces[$5]+=1}
    END {for (interface in interfaces){print(interface)}}
  '
);
for interface in $interfaces; do
  echo "Clearing ARP cache for $interface";
  sudo ip link set arp off dev $interface;
  sudo ip link set arp on  dev $interface;
done

Note: The semicolons allow you to condense this command into a oneliner, but it looks terrible in a code block on SO.

Example output on Raspbian

pi@raspberrypi:~ $ arp -n
Address                  HWtype  HWaddress           Flags Mask            Iface
10.0.0.1                 ether   58:19:f8:0d:57:aa   C                     wlan0
10.0.0.159               ether   88:e9:fe:84:82:c8   C                     wlan0

pi@raspberrypi:~ $ interfaces=$( arp -n | awk ' NR == 1 {next} {interfaces[$5]+=1} END {for (interface in interfaces){print(interface)}} '); for interface in $interfaces; do echo "Clearing ARP cache for $interface"; sudo ip link set arp off dev $interface; sudo ip link set arp on  dev $interface; done
Clearing ARP cache for wlan0

pi@raspberrypi:~ $ arp -n
Address                  HWtype  HWaddress           Flags Mask            Iface
10.0.0.159               ether   88:e9:fe:84:82:c8   C                     wlan0

Your routing table isn't being ignored, exactly. It's being overruled by a higher-priority routing table.

What's Going On

The routing table you see when you type ip route show isn't the only routing table the kernel uses. In fact, there are three routing tables by default, and they are searched in the order shown by the ip rule command:

# ip rule show
0:      from all lookup local
32766:  from all lookup main
32767:  from all lookup default

The table you're most familiar with is main, but the highest-priority routing table is local. This table is managed by the kernel to keep track of local and broadcast routes: in other words, the local table tells the kernel how to route to the addresses of its own interfaces. It looks something like this:

# ip route show table local
broadcast 127.0.0.0 dev lo  proto kernel  scope link  src 127.0.0.1
local 127.0.0.0/8 dev lo  proto kernel  scope host  src 127.0.0.1
local 127.0.0.1 dev lo  proto kernel  scope host  src 127.0.0.1
broadcast 127.255.255.255 dev lo  proto kernel  scope link  src 127.0.0.1
broadcast 192.168.1.0 dev eth0  proto kernel  scope link  src 192.168.1.2
local 192.168.1.1 dev tun0  proto kernel  scope host  src 192.168.1.1
local 192.168.1.2 dev eth0  proto kernel  scope host  src 192.168.1.2
broadcast 192.168.1.255 dev eth0  proto kernel  scope link  src 192.168.1.2

Check out that line referencing tun0. That's what's causing your strange results from route get. It says 192.168.1.1 is a local address, which means if we want to send an ARP reply to 192.168.1.1, it's easy; we send it to ourself. And since we found a route in the local table, we stop searching for a route, and don't bother checking the main or default tables.

Why multiple tables?

At a minimum, it's nice to be able to type ip route and not see all those "obvious" routes cluttering the display (try typing route print on a Windows machine). It can also serve as some minimal protection against misconfiguration: even if the main routing table has gotten mixed up, the kernel still knows how to talk to itself.

(Why keep local routes in the first place? So the kernel can use the same lookup code for local addresses as it does for everything else. It makes things simpler internally.)

There are other interesting things you can do with this multiple-table scheme. In particular, you can add your own tables, and specify rules for when they are searched. This is called "policy routing", and if you've ever wanted to route a packet based on its source address, this is how to do it in Linux.

If you're doing especially tricky or experimental things, you can add or remove local routes yourself by specifying table local in the ip route command. Unless you know what you're doing, though, you're likely to confuse the kernel. And of course, the kernel will still continue to add and remove its own routes, so you have to watch to make sure yours don't get overwritten.

Finally, if you want to see all of the routing tables at once:

# ip route show table all

For more info, check out the ip-rule(8) man page or the iproute2 docs. You might also try the Advanced Routing and Traffic Control HOWTO for some examples of what you can do.