Remember, a rocket ejects its exhaust at a fixed velocity relative to the ship. Multiply that by the flow rate (mass per second) and you've got a certain amount of thrust (which, divided by the mass of the ship, is your acceleration). But you've only got a certain amount of propellant on board, and once it runs out, you can't go any faster. You've reached top speed. Changing the flow rate of the rocket does not, in fact, change this speed. If you throttle back to half the maximum flow rate, you can accelerate for twice as long, but you only accelerate half as much, so you end up accelerating to the same speed regardless.
The actual top speed of a rocket can be calculated using the Tsiolkovsky rocket equation:
Δv = Ve * ln(R)
where Δv is the top speed, Ve is the exhaust velocity, and R is the mass ratio (mass of fully fuelled ship / mass of empty ship).
Note that the absolute mass of the ship isn't a factor: a ship that's twice as massive can carry twice as much propellant, but only gets half as much acceleration for a given thrust, so it balances out. The mass ratio is important, because the ship constantly gets lighter as it consumes propellant. Carrying more propellant enables you to go faster, but only after you've consumed most of it. Also note that increasing your speed requires increasing the mass ratio exponentially; this is why most space rockets look like giant propellant tanks with a tiny ship on top and a tiny rocket motor on the bottom. It's also the reason for multi-stage rockets: dumping spent engines reduces the rocket's empty weight, and so increases the mass ratio even further.
It's not brain surgery.