Pittsburgh and Seattle each spent $50,000 in order to select Rodriguez and Flores, respectively. The players need to remain on their club's active roster for the entirety of the 2011 season, or be offered back to Cleveland for half the selection cost.
Atkins was not surprised Pittsburgh opted to give Rodriguez a shot.
"We knew that he certainly could be taken," Atkins said. "He has a chance to be a solid Major League contributor. I'm happy for him, happy for the opportunity that he's going to get. We're sorry to lose him."
Rodriguez, who will turn 26 later this month, is a versatile infielder who has experience at second base, shortstop and third, as well as some outfield. Last year at Triple-A Columbus, he hit .293 with a .372 on-base percentage, 12 home runs and 46 RBIs. That followed a stint with Double-A Akron, where he hit at a .317 clip over 21 games.
"He's a guy that will compete to make our club as our utility guy," Pirates general manager Neal Huntington said. "He has solid defense at shortstop. He can swing the bat a little bit."
Atkins said the Tribe's depth at the middle-infield positions played a role in the decision to leave Rodriguez off the 40-man roster.
"That certainly contributes to it," Atkins said. "You're always factoring in what the upside of the player is, what your alternatives are at that position. Those two things are the determining factors."
Flores, 21, was more of a surprise pick in the second overall slot.
A year ago, the Venezuelan righty fashioned a 2.14 ERA with 51 strikeouts and seven walks over 42 innings, but he spent the whole season with low-Class A Lake County. Atkins said Flores projected to open this season with high-Class A Kinston or Double-A Akron in Cleveland's system.
"He's a good pitcher," Atkins said. "He's a good young pitcher that was in the Midwest League. [I'm not surprised he was drafted] from a talent standpoint, but it's unusual for a guy to be taken out of low-A ball."
Entering the Rule 5 Draft, the Indians felt there was a chance that right-hander Adam Miller would be selected.
Miller -- a first-round pick by Cleveland in the 2003 First-Year Player Draft -- is working his way back from four finger surgeries, but he is trying to carve out a role as a reliever. Miller was not selected in the Rule 5 Draft on Thursday, so he will continue his comeback attempt with the Indians.
The Tribe's front office met on Wednesday to discuss making a move in order to vacate a spot on the 40-man roster in preparation for a potential Rule 5 addition. Cleveland ultimately decided to stand pat, leaving its roster at capacity and sitting out of the selection process.