Yes—carrying your DSLR regularly is generally fine, and it’s usually better to use the camera than leave it sitting at home. A mid-range DSLR is built to handle normal day-to-day use, so the main thing is simply to avoid unnecessary shocks and rough handling.

Your setup already sounds sensible: a snug camera bag inside a padded backpack with the lens left mounted reduces handling and helps protect the camera. If you ride a bike, just be mindful of bumps and impacts.

Dust on or around the eyepiece is usually more of an annoyance than a real problem. If the lens stays attached, dust is much less likely to get inside the camera body or onto the sensor. Dust or a hair in the viewfinder area may be visible when looking through it, but it typically won’t affect image quality.

Closing the quick-access flap may help keep out some dust and debris, so it’s a reasonable precaution, but the bigger factors are keeping the camera protected from knocks and avoiding lens changes in dusty conditions.

In short: take it with you, use normal care, keep the lens securely attached, and protect it from impacts.