Alma was afraid to rock the boat. Period.
I think Alma didn't say anything initially because she frankly didn't know what the ramifications of what she was seeing would be. Even after Ennis stayed out all night and then hurriedly packed for a fishing trip, Alma still wouldn't say anything because she didn't understand what it all meant and how it would affect her and the girls. She knew that Jack was from Texas; he lived far away from them. For all she knew at the time, the reunion was just a one-shot thing, so she keeps her mouth shut and plays it safe. She had no way of knowing that Ennis would continue to see Jack. I think she chose to just wait it out, hoping that whatever it was, Ennis would get it out of his system and things would go back to how they were before. After all, she knew that Ennis wasn't running off with other guys, only Jack, and Jack lived too far away to be a real threat. Plus, she knew he had a wife and a baby. Since he was seemingly attached, Alma felt safe. Of course, she was in denial, but she couldn't know everything in the beginning.
I think Alma just got herself in the habit of hiding her head in the sand and denying what was going on. Ennis only saw Jack a couple of times of year, and she could deal with it because he always came back to her and the girls. But she didn't dare confront Ennis because she didn't want to know. Even after she tied the note to the fishing line and Ennis failed her little test, she still wouldn't confront him, again because she did not want to know the truth.
Of course, her denial got harder to bear as the years went on and Jack continued to be a presence in Ennis's life. She saw the anticipation on Ennis's face when he was leaving for his fishing trips, and she saw how happy he was when he returned. Hard as she tried, she couldn't get that kind of reaction out of him, and she was frustrated because she was doing all she could.
Divorce seemed to be the logical step, but it wasn't only because of the fishing trips. Alma had a whole laundry list of complaints about Ennis; his time with Jack was only one of them. But I think that Monroe played a part in Alma's decision to leave Ennis. Alma appears to be the type of woman who wouldn't leave her husband unless she had someone to run to. Yes, she was playing it safe once again, but she was also looking out for the well-being of her children. She wanted a good life for them.
I don't believe that Alma intended to confront Ennis at Thanksgiving. I think she was just annoyed and jealous that the girls were so happy to be with Ennis. If Ennis hadn't made his "Once burned" comment, Alma most likely never would have said what she said. In Alma's defense, she was probably tired and cranky and feeling unappreciated. Being pregnant, her hormones were probably playing havoc with her as well.