Instead, it's a compliment.
Agents who do things just to be "nice" won't be in business very long. A request like this means the agent thinks the book is promising.
Now it's up to the writer to decide whether the suggested changes fit with the book the writer is writing. After all, it's the writer's book, not the agent's. The writer has lived it with it for a year or two, the agent for a couple of hours. On the other hand, the agent has seen a lot more come across her desk and may be able to put her finger on the wrong parts without even having to give it much thought.