SANTA CLARA — The 49ers are doing their best to remain optimistic despite their winless start in coach Kyle Shanahan’s first season.

They’ve fallen by eight points combined over their past three games, all to NFC West rivals, while they wade through a season defined by low expectations.

“If you look at the tape, there’s lots of things to be encouraged about,” Shanahan said. “It’s tough as a coach to ever turn it on and feel like you’re not doing anything good, but I haven’t felt that way really once after any of the four games. I know we’ve got to do better and we’ve got to clean a lot of stuff up, but that’s the goal, to get better each week.”

Shanahan and new general manager John Lynch signed matching six-year contracts when they were hired in the offseason, making 2017 the start of an organization-wide reconstruction project. Thirty-three of the team’s players are new to the roster and it’s clear the growing pains have been paramount during the 0-4 start.

The 49ers lead the NFL in dropped passes, according to Pro Football Focus, while also committing the most penalties.

Quarterback Brian Hoyer has thrown an interception in all four games and opponents have scored points in each possession following San Francisco’s six turnovers.

Ahead Sunday is a trip to Indianapolis (1-3), marking the second game of three in a row away from the Bay Area. Hoyer’s play has led to chatter about his job security while fans ponder the thought of third-round draft pick C.J. Beathard, who won the backup job over veteran Matt Barkley in the preseason.

Hoyer helped orchestrate a 17-play drive in overtime Sunday in Arizona that led to a 23-yard field goal after a failed trip to the red zone. The Cardinals got the ball back and won the game when Larry Fitzgerald caught a 19-yard touchdown pass with 32 seconds remaining.

A touchdown for San Francisco would have won it. Instead, the 49ers left Arizona having failed to get in the end zone in three of their four contests this season.

“It’s encouraging because you can see that you’re only a few plays away. But it’s also tough to swallow because you know that you’re that close,” Hoyer said. “We’re 0-4. It’s a results business. No one’s going to care that we almost won that game, or almost won this game. You only care if you win. It’s tough, but you can either go in one of two directions.”

NOTES

Receiver Marquise Goodwin was no longer wearing a noncontact jersey during practice Thursday as he did Wednesday, indicating he’s progressing through the concussion protocol after leaving the Cardinals game in the first half. Carlos Hyde (injured side) was limited after playing Sunday, as was his backup Matt Breida, who’s working through an ankle injury.

Rookie safety Adrian Colbert (hamstring) and linebacker Dekoda Watson (groin) missed practice for the second day in a row and appear unlikely to play Sunday. Both are key players on special teams.