Some timers have an in-line fuse between the timer and the battery, if you cut out the fuse and wire it direct the timer no longer works. My question is why? How can the timer tell if the fuse is there or not if you direct wire it to the battery?

Shouldn't matter w/fuse or no fuse as long as the wires are connected properly.

I would not have thought it would have mattered either but when I cut the inline fuse out, wired it together and connected it to the battery the timer would not come on. I disconnected it and rewired a new inline fuse connected it to the battery and the timer came on.

It has no way of knowing. Regarding operating without a fuse, keep in mind the fuse is there to keep a failure from destroying the rest of your timer. Operating without it isn’t recommended.

I agree with this statement.

What type of fuse is it?

Sounds like you have a bad connection, without the fuse. Some of my timers have fuses, some do not. As already mentioned, they were put there for a reason. I carry some spares in my truck.

What brand timer is it? That'll help us understand what's going on with it. Most of your better timers will have a fuse of some sort, being inline or accessible inside the timer unit itself. If you cut the fuse out, and reconnect it properly, it should still work, but remember the fuse is there for a reason and without it you stand the chance of ruining the timer without that protection.

Believe it was one of the simple set timers, green with orange buttons...the fuse was one of the round glass tubes. I replaced it with a two prong blade plug 10A fuse.

A fuse is simply a wire that will melt if too much current is applied. There's no way for the downstream electrical device to know it is there unless the fuse block has some kind of circuitry in it to send a specific signal downstream with the timer looking for it. I've never seen such a fuse block and I've done a lot of electrical work.