It sounds as if you need to learn a little more theory -- a musical phrase can have a mixture of note lengths, and an unchanging tempo.
A metronome provides you with a regular pulse. You are not necessarily expected to play a note on each tick, and often you'll also want to play notes in-between ticks.
As a simple example, if you set the metronome to tick on quarter notes, and the phrase you're practising starts with two eighth notes, then you would play the first eighth note on a tick, and the second eighth note halfway between that and the next tick.
Three ways in which a metronome can help with practice:
Improving your basic rhythm
It's easy for beginners to fall into the trap of just trying to get the notes out in the right order, speeding up for the easy bits, slowing down for the difficult bits. Practising with a metronome helps train yourself to maintain a tempo.
There's nothing wrong with expressive tempo changes, of course. In some styles of music, it's important to slow down and speed up, for expression. But that's not the same as speeding up for the easy bits and slowing down for the hard bits (indeed, a great musician will often slow down to coax more feel out of the "slow" parts of the music, and speed up to get maximum effect from the lively parts).
Building up to playing complex parts at fast tempos
A good way to learn complex parts, is to learn them at a slow tempo, then incrementally increase the tempo. There are two challenges here:
- The temptation to go too fast, when we're supposed to be practising slow.
- The tendency to slow down for the fiddly part, without realising it.
Following a metronome helps with both of these.
Improving your "internal metronome"
One great exercise, for testing and improving your innate sense of rhythm and tempo, is to keep halving the tempo of the metronome, while playing your part at the same tempo.
So, if you're practising something at 120bpm, start the metronome at 120bpm. You get a tick every beat. Get comfortable playing a part over that. It should be pretty easy.
Then set the metronome to 60bpm. Now you get a tick for the first and third beat of every bar, but you have to "feel" the second and fourth beats. Keep playing. It should still be quite easy.
Then set the metronome to 30bpm. Now you only get a tick on the first beat of each bar. You have to concentrate harder to keep to the rhythm. Your challenge is to stay in synch, so the metronome tick continues to coincide with your playing. If your metronome has slow enough settings, you can have one tick every two bars, or every four bars - and if you can stay in synch with that, you're good.
This exercise makes good use of a metronome, while getting away from the robotic feel that some people fear from metronomes.
You can also practice with drum machines, for something with more feel than a metronome.